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(-) Description

Title :  HMGB1-FACILITATED P53 DNA BINDING OCCURS VIA HMG-BOX/P53 TRANSACTIVATION DOMAIN INTERACTION AND IS REGULATED BY THE ACIDIC TAIL
 
Authors :  J. P. Rowell, K. L. Simpson, K. Stott, M. Watson, J. O. Thomas
Date :  12 Sep 12  (Deposition) - 31 Oct 12  (Release) - 26 Dec 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Hmg, P53, Tad, Nuclear Protein-Antitumour Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. P. Rowell, K. L. Simpson, K. Stott, M. Watson, J. O. Thomas
Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-Box/P53 Transactivation Domain Interaction, Regulated By The Acidic Tail.
Structure V. 20 2014 2012
PubMed-ID: 23063560  |  Reference-DOI: 10.1016/J.STR.2012.09.004

(-) Compounds

Molecule 1 - HIGH MOBILITY GROUP PROTEIN B1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7-7 HMG1-A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneHMG1, HMGB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHIGH MOBILITY GROUP PROTEIN 1, HMG-1
 
Molecule 2 - CELLULAR TUMOR ANTIGEN P53
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET16B-P53(1-93)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneP53, TP53
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANTIGEN NY-CO-13, PHOSPHOPROTEIN P53, TUMOR SUPPRESSOR P53

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2LY4)

(-) Sites  (0, 0)

(no "Site" information available for 2LY4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LY4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LY4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (44, 44)

NMR Structure (44, 44)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_046451G11RHMGB1_HUMANUnclassified  ---AG10R
02UniProtVAR_044549S15RP53_HUMANUnclassified  ---BS15R
03UniProtVAR_044550Q16LP53_HUMANUnclassified  ---BQ16L
04UniProtVAR_044551E17DP53_HUMANUnclassified  ---BE17D
05UniProtVAR_044552K24NP53_HUMANUnclassified  ---BK24N
06UniProtVAR_044553E28AP53_HUMANUnclassified  ---BE28A
07UniProtVAR_044554V31IP53_HUMANUnclassified201753350BV31I
08UniProtVAR_044555S33TP53_HUMANUnclassified  ---BS33T
09UniProtVAR_044556P34LP53_HUMANUnclassified  ---BP34L
10UniProtVAR_005852L35FP53_HUMANUnclassified121912661BL35F
11UniProtVAR_044557P36LP53_HUMANUnclassified587781866BP36L
12UniProtVAR_044558S37PP53_HUMANUnclassified  ---BS37P
13UniProtVAR_044559S37TP53_HUMANUnclassified  ---BS37T
14UniProtVAR_044560A39PP53_HUMANUnclassified  ---BA39P
15UniProtVAR_044561A39VP53_HUMANUnclassified  ---BA39V
16UniProtVAR_044562D42YP53_HUMANUnclassified  ---BD42Y
17UniProtVAR_005853L43SP53_HUMANUnclassified  ---BL43S
18UniProtVAR_044563M44IP53_HUMANUnclassified  ---BM44I
19UniProtVAR_044564M44TP53_HUMANUnclassified  ---BM44T
20UniProtVAR_044565M44VP53_HUMANUnclassified  ---BM44V
21UniProtVAR_044566L45MP53_HUMANUnclassified  ---BL45M
22UniProtVAR_044567S46FP53_HUMANUnclassified  ---BS46F
23UniProtVAR_044568S46PP53_HUMANUnclassified876659630BS46P
24UniProtVAR_044569P47LP53_HUMANUnclassified  ---BP47L
25UniProtVAR_014632P47SP53_HUMANPolymorphism1800371BP47S
26UniProtVAR_044570D48GP53_HUMANUnclassified  ---BD48G
27UniProtVAR_044571D49HP53_HUMANUnclassified587780728BD49H
28UniProtVAR_044572D49NP53_HUMANUnclassified587780728BD49N
29UniProtVAR_044573D49YP53_HUMANUnclassified  ---BD49Y
30UniProtVAR_044574Q52HP53_HUMANUnclassified  ---BQ52H
31UniProtVAR_005854W53CP53_HUMANUnclassified  ---BW53C
32UniProtVAR_044575W53GP53_HUMANUnclassified  ---BW53G
33UniProtVAR_044576F54LP53_HUMANUnclassified  ---BF54L
34UniProtVAR_044577F54YP53_HUMANUnclassified  ---BF54Y
35UniProtVAR_044578E56KP53_HUMANUnclassified  ---BE56K
36UniProtVAR_044579E56VP53_HUMANUnclassified  ---BE56V
37UniProtVAR_044580P58QP53_HUMANUnclassified  ---BP58Q
38UniProtVAR_044581P58TP53_HUMANUnclassified  ---BP58T
39UniProtVAR_044582G59CP53_HUMANUnclassified  ---BG59C
40UniProtVAR_044583G59DP53_HUMANUnclassified  ---BG59D
41UniProtVAR_045783G59NP53_HUMANUnclassified  ---BG59N
42UniProtVAR_044584P60LP53_HUMANUnclassified  ---BP60L
43UniProtVAR_044585P60QP53_HUMANUnclassified  ---BP60Q
44UniProtVAR_005855P60SP53_HUMANUnclassified  ---BP60S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (44, 44)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_046451G11RHMGB1_HUMANUnclassified  ---AG10R
02UniProtVAR_044549S15RP53_HUMANUnclassified  ---BS15R
03UniProtVAR_044550Q16LP53_HUMANUnclassified  ---BQ16L
04UniProtVAR_044551E17DP53_HUMANUnclassified  ---BE17D
05UniProtVAR_044552K24NP53_HUMANUnclassified  ---BK24N
06UniProtVAR_044553E28AP53_HUMANUnclassified  ---BE28A
07UniProtVAR_044554V31IP53_HUMANUnclassified201753350BV31I
08UniProtVAR_044555S33TP53_HUMANUnclassified  ---BS33T
09UniProtVAR_044556P34LP53_HUMANUnclassified  ---BP34L
10UniProtVAR_005852L35FP53_HUMANUnclassified121912661BL35F
11UniProtVAR_044557P36LP53_HUMANUnclassified587781866BP36L
12UniProtVAR_044558S37PP53_HUMANUnclassified  ---BS37P
13UniProtVAR_044559S37TP53_HUMANUnclassified  ---BS37T
14UniProtVAR_044560A39PP53_HUMANUnclassified  ---BA39P
15UniProtVAR_044561A39VP53_HUMANUnclassified  ---BA39V
16UniProtVAR_044562D42YP53_HUMANUnclassified  ---BD42Y
17UniProtVAR_005853L43SP53_HUMANUnclassified  ---BL43S
18UniProtVAR_044563M44IP53_HUMANUnclassified  ---BM44I
19UniProtVAR_044564M44TP53_HUMANUnclassified  ---BM44T
20UniProtVAR_044565M44VP53_HUMANUnclassified  ---BM44V
21UniProtVAR_044566L45MP53_HUMANUnclassified  ---BL45M
22UniProtVAR_044567S46FP53_HUMANUnclassified  ---BS46F
23UniProtVAR_044568S46PP53_HUMANUnclassified876659630BS46P
24UniProtVAR_044569P47LP53_HUMANUnclassified  ---BP47L
25UniProtVAR_014632P47SP53_HUMANPolymorphism1800371BP47S
26UniProtVAR_044570D48GP53_HUMANUnclassified  ---BD48G
27UniProtVAR_044571D49HP53_HUMANUnclassified587780728BD49H
28UniProtVAR_044572D49NP53_HUMANUnclassified587780728BD49N
29UniProtVAR_044573D49YP53_HUMANUnclassified  ---BD49Y
30UniProtVAR_044574Q52HP53_HUMANUnclassified  ---BQ52H
31UniProtVAR_005854W53CP53_HUMANUnclassified  ---BW53C
32UniProtVAR_044575W53GP53_HUMANUnclassified  ---BW53G
33UniProtVAR_044576F54LP53_HUMANUnclassified  ---BF54L
34UniProtVAR_044577F54YP53_HUMANUnclassified  ---BF54Y
35UniProtVAR_044578E56KP53_HUMANUnclassified  ---BE56K
36UniProtVAR_044579E56VP53_HUMANUnclassified  ---BE56V
37UniProtVAR_044580P58QP53_HUMANUnclassified  ---BP58Q
38UniProtVAR_044581P58TP53_HUMANUnclassified  ---BP58T
39UniProtVAR_044582G59CP53_HUMANUnclassified  ---BG59C
40UniProtVAR_044583G59DP53_HUMANUnclassified  ---BG59D
41UniProtVAR_045783G59NP53_HUMANUnclassified  ---BG59N
42UniProtVAR_044584P60LP53_HUMANUnclassified  ---BP60L
43UniProtVAR_044585P60QP53_HUMANUnclassified  ---BP60Q
44UniProtVAR_005855P60SP53_HUMANUnclassified  ---BP60S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.HMGB1_HUMAN9-79
95-163
  1A:8-78
-
2HMG_BOX_1PS00353 HMG box A DNA-binding domain signature.HMGB1_HUMAN41-52  1A:40-51
NMR Structure * (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.HMGB1_HUMAN9-79
95-163
  1A:8-78
-
2HMG_BOX_1PS00353 HMG box A DNA-binding domain signature.HMGB1_HUMAN41-52  1A:40-51

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002693051aENSE00001146308chr17:7590856-7590695162P53_HUMAN-00--
1.3aENST000002693053aENSE00002194362chr17:7579940-7579839102P53_HUMAN1-25251B:14-2512
1.3dENST000002693053dENSE00001710434chr17:7579721-757970022P53_HUMAN25-3281B:25-328
1.4bENST000002693054bENSE00001718735chr17:7579590-7579312279P53_HUMAN33-125931B:33-6028
1.5dENST000002693055dENSE00001255919chr17:7578554-7578371184P53_HUMAN126-187620--
1.6aENST000002693056aENSE00001255912chr17:7578289-7578177113P53_HUMAN187-224380--
1.7bENST000002693057bENSE00001665758chr17:7577608-7577499110P53_HUMAN225-261370--
1.8ENST000002693058ENSE00001789298chr17:7577155-7577019137P53_HUMAN261-307470--
1.9ENST000002693059ENSE00002149110chr17:7576926-757685374P53_HUMAN307-331250--
1.11ENST0000026930511ENSE00001728015chr17:7574033-7573927107P53_HUMAN332-367360--
1.12dENST0000026930512dENSE00001757276chr17:7573008-75717201289P53_HUMAN367-393270--

2.4ENST000003994944ENSE00001538645chr13:31039379-31039210170HMGB1_HUMAN-00--
2.5dENST000003994945dENSE00001384053chr13:31037831-31037668164HMGB1_HUMAN1-50501A:1-4949
2.5gENST000003994945gENSE00000906655chr13:31037489-31037344146HMGB1_HUMAN51-99491A:50-8334
2.6bENST000003994946bENSE00001381337chr13:31036849-31036675175HMGB1_HUMAN99-157590--
2.7eENST000003994947eENSE00001538641chr13:31035670-31035044627HMGB1_HUMAN158-215580--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:83
 aligned with HMGB1_HUMAN | P09429 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:83
                                    11        21        31        41        51        61        71        81   
           HMGB1_HUMAN    2 GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE 84
               SCOP domains d2ly4a_ A: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------R------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------HMG_BOX_2  PDB: A:8-78 UniProt: 9-79                                   ----- PROSITE (1)
                PROSITE (2) ---------------------------------------HMG_BOX_1   -------------------------------- PROSITE (2)
               Transcript 2 Exon 2.5d  PDB: A:1-49 UniProt: 1-50 [INCOMPLETE]Exon 2.5g  PDB: A:50-83            Transcript 2
                  2ly4 A  1 GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE 83
                                    10        20        30        40        50        60        70        80   

Chain B from PDB  Type:PROTEIN  Length:47
 aligned with P53_HUMAN | P04637 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:47
                                    23        33        43        53       
             P53_HUMAN   14 LSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP 60
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ................................hhhhhh......... Sec.struct. author
             SAPs(SNPs) (1) -RLD------N---A--I-TLFLP-P--YSIMFLGH--HCL-K-QCL SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------T-V----T-PS-N---GY-V-TDQ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ------------------------------V----Y---------NS SAPs(SNPs) (3)
                    PROSITE ----------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a   -------Exon 1.4b  PDB: B:33-60      Transcript 1 (1)
           Transcript 1 (2) -----------1.3d    ---------------------------- Transcript 1 (2)
                  2ly4 B 14 LSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP 60
                                    23        33        43        53       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LY4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LY4)

(-) Gene Ontology  (226, 241)

NMR Structure(hide GO term definitions)
Chain A   (HMGB1_HUMAN | P09429)
molecular function
    GO:0019958    C-X-C chemokine binding    Interacting selectively and non-covalently with a C-X-C chemokine; C-X-C chemokines have a single amino acid between the first two cysteines of the characteristic four cysteine motif.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0070182    DNA polymerase binding    Interacting selectively and non-covalently with a DNA polymerase.
    GO:0050786    RAGE receptor binding    Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
    GO:0000405    bubble DNA binding    Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA.
    GO:0010858    calcium-dependent protein kinase regulator activity    Modulates the activity of a calcium-dependent protein kinase, an enzyme which phosphorylates a protein in a calcium-dependent manner.
    GO:0042056    chemoattractant activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0000400    four-way junction DNA binding    Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.
    GO:0001530    lipopolysaccharide binding    Interacting selectively and non-covalently with lipopolysaccharide.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0001786    phosphatidylserine binding    Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030295    protein kinase activator activity    Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0097100    supercoiled DNA binding    Interacting selectively and non-covalently with supercoiled DNA. For example, during replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0032392    DNA geometric change    The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases.
    GO:0051103    DNA ligation involved in DNA repair    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0035711    T-helper 1 cell activation    The change in morphology and behavior of a T-helper 1 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0045063    T-helper 1 cell differentiation    The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma.
    GO:0033151    V(D)J recombination    The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
    GO:0002218    activation of innate immune response    Any process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species.
    GO:0032147    activation of protein kinase activity    Any process that initiates the activity of an inactive protein kinase.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0006309    apoptotic DNA fragmentation    The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0031497    chromatin assembly    The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
    GO:0002407    dendritic cell chemotaxis    The movement of a dendritic cell in response to an external stimulus.
    GO:0035767    endothelial cell chemotaxis    The directed movement of an endothelial cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0001935    endothelial cell proliferation    The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
    GO:0001654    eye development    The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0002437    inflammatory response to antigenic stimulus    An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0002281    macrophage activation involved in immune response    A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
    GO:0001773    myeloid dendritic cell activation    The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0043371    negative regulation of CD4-positive, alpha-beta T cell differentiation    Any process that stops, prevents, or reduces the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation.
    GO:0017055    negative regulation of RNA polymerase II transcriptional preinitiation complex assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
    GO:2000426    negative regulation of apoptotic cell clearance    Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic cell clearance.
    GO:0043537    negative regulation of blood vessel endothelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
    GO:0032689    negative regulation of interferon-gamma production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0097350    neutrophil clearance    The selective elimination of senescent neutrophils from the body by autoregulatory mechanisms.
    GO:0002270    plasmacytoid dendritic cell activation    A change in the morphology or behavior of a plasmacytoid dendritic cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0051106    positive regulation of DNA ligation    Any process that activates or increases the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0046330    positive regulation of JNK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:1901224    positive regulation of NIK/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of NIK/NF-kappaB signaling.
    GO:0042104    positive regulation of activated T cell proliferation    Any process that activates or increases the rate or extent of activated T cell proliferation.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:2001200    positive regulation of dendritic cell differentiation    Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation.
    GO:0045819    positive regulation of glycogen catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.
    GO:0045089    positive regulation of innate immune response    Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0032727    positive regulation of interferon-alpha production    Any process that activates or increases the frequency, rate, or extent of interferon-alpha production.
    GO:0032728    positive regulation of interferon-beta production    Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
    GO:0050718    positive regulation of interleukin-1 beta secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
    GO:0050716    positive regulation of interleukin-1 secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 from a cell.
    GO:0032733    positive regulation of interleukin-10 production    Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
    GO:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    GO:2000778    positive regulation of interleukin-6 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.
    GO:0032425    positive regulation of mismatch repair    Any process that activates or increases the frequency, rate or extent of mismatch repair.
    GO:0090026    positive regulation of monocyte chemotaxis    Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
    GO:0045639    positive regulation of myeloid cell differentiation    Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:1903672    positive regulation of sprouting angiogenesis    Any process that activates or increases the frequency, rate or extent of sprouting angiogenesis.
    GO:0034137    positive regulation of toll-like receptor 2 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 2 signaling pathway.
    GO:0034145    positive regulation of toll-like receptor 4 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 4 signaling pathway.
    GO:0034165    positive regulation of toll-like receptor 9 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 9 signaling pathway.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    GO:0090303    positive regulation of wound healing    Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0002840    regulation of T cell mediated immune response to tumor cell    Any process that modulates the frequency, rate, or extent of a T cell mediated immune response to tumor cell.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:2000819    regulation of nucleotide-excision repair    Any process that modulates the frequency, rate or extent of nucleotide-excision repair.
    GO:0045859    regulation of protein kinase activity    Any process that modulates the frequency, rate or extent of protein kinase activity.
    GO:0032072    regulation of restriction endodeoxyribonuclease activity    Any process that modulates the frequency, rate or extent of a restriction endodeoxyribonuclease activity, the catalysis of endonucleolytic cleavage of DNA in a site-specific manner, resulting in double-strand breaks.
    GO:0002643    regulation of tolerance induction    Any process that modulates the frequency, rate, or extent of tolerance induction.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:1990774    tumor necrosis factor secretion    The regulated release of tumor necrosis factor from a cell. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

Chain B   (P53_HUMAN | P04637)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0001046    core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0035035    histone acetyltransferase binding    Interacting selectively and non-covalently with the enzyme histone acetyltransferase.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0051721    protein phosphatase 2A binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 2A.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    GO:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030330    DNA damage response, signal transduction by p53 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0006978    DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21 (also known as WAF1, CIP1 and SDI1) or any equivalent protein, in response to the detection of DNA damage.
    GO:0000733    DNA strand renaturation    The identification and annealing of complementary base pairs in single-strand DNA.
    GO:0006983    ER overload response    The series of molecular signals generated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum and leading to activation of transcription by NF-kappaB.
    GO:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0007569    cell aging    An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0034644    cellular response to UV    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0042149    cellular response to glucose starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of glucose.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0071479    cellular response to ionizing radiation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
    GO:0031497    chromatin assembly    The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
    GO:0048512    circadian behavior    The specific behavior of an organism that recurs with a regularity of approximately 24 hours.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0043153    entrainment of circadian clock by photoperiod    The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
    GO:0097193    intrinsic apoptotic signaling pathway    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
    GO:0072332    intrinsic apoptotic signaling pathway by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered.
    GO:0042771    intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0031571    mitotic G1 DNA damage checkpoint    A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G1/S transition of the cell cycle in response to DNA damage.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0048147    negative regulation of fibroblast proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    GO:0051097    negative regulation of helicase activity    Any process that stops or reduces the activity of a helicase.
    GO:0051974    negative regulation of telomerase activity    Any process that stops or reduces the activity of the enzyme telomerase, which catalyzes of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0097252    oligodendrocyte apoptotic process    Any apoptotic process in an oligodendrocyte. Oligodendrocytes belong to a class of large neuroglial (macroglial) cells in the central nervous system, where they form the insulating myelin sheath of axons.
    GO:0090403    oxidative stress-induced premature senescence    A cellular senescence process associated with the dismantling of a cell as a response to oxidative stress, e.g. high levels of reactive oxygen species, such as superoxide anions, hydrogen peroxide, and hydroxyl radicals.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0071158    positive regulation of cell cycle arrest    Any process that increases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:1900119    positive regulation of execution phase of apoptosis    Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0031065    positive regulation of histone deacetylation    Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones.
    GO:2001244    positive regulation of intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0046827    positive regulation of protein export from nucleus    Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
    GO:1900740    positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
    GO:0032461    positive regulation of protein oligomerization    Any process that activates or increases the frequency, rate or extent of protein oligomerization.
    GO:2000379    positive regulation of reactive oxygen species metabolic process    Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0090200    positive regulation of release of cytochrome c from mitochondria    Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:0070245    positive regulation of thymocyte apoptotic process    Any process that activates or increases the frequency, rate or extent of thymocyte death by apoptotic process.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:1990440    positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an endoplasmic reticulum stress.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:1902749    regulation of cell cycle G2/M phase transition    Any process that modulates the frequency, rate or extent of cell cycle G2/M phase transition.
    GO:0046902    regulation of mitochondrial membrane permeability    Any process that modulates the frequency, rate or extent of the passage or uptake of molecules by the mitochondrial membrane.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0090399    replicative senescence    A cell aging process associated with the dismantling of a cell as a response to telomere shortening and/or cellular aging.
    GO:0010165    response to X-ray    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0010332    response to gamma radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0005657    replication fork    The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.
    GO:0005669    transcription factor TFIID complex    A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HMGB1_HUMAN | P094292rtu 2yrq
        P53_HUMAN | P046371a1u 1aie 1c26 1dt7 1gzh 1h26 1hs5 1jsp 1kzy 1ma3 1olg 1olh 1pes 1pet 1sae 1saf 1sak 1sal 1tsr 1tup 1uol 1xqh 1yc5 1ycq 1ycr 1ycs 2ac0 2ady 2ahi 2ata 2b3g 2bim 2bin 2bio 2bip 2biq 2f1x 2fej 2foj 2foo 2gs0 2h1l 2h2d 2h2f 2h4f 2h4h 2h4j 2h59 2j0z 2j10 2j11 2j1w 2j1x 2j1y 2j1z 2j20 2j21 2k8f 2l14 2mej 2mwo 2mwp 2mwy 2mzd 2ocj 2pcx 2ruk 2vuk 2wgx 2x0u 2x0v 2x0w 2xwr 2ybg 2ydr 2z5s 2z5t 3d05 3d06 3d07 3d08 3d09 3d0a 3dab 3dac 3igk 3igl 3kmd 3kz8 3lw1 3oq5 3pdh 3q01 3q05 3q06 3sak 3tg5 3ts8 3zme 4agl 4agm 4agn 4ago 4agp 4agq 4buz 4bv2 4fz3 4hfz 4hje 4ibq 4ibs 4ibt 4ibu 4ibv 4ibw 4iby 4ibz 4ijt 4kvp 4lo9 4loe 4lof 4mzi 4mzr 4qo1 4rp6 4rp7 4x34 4xr8 4zzj 5a7b 5ab9 5aba 5aoi 5aoj 5aok 5aol 5aom 5bua 5ecg 5g4m 5g4n 5g4o 5hou 5hp0 5hpd 5lap 5lgy 5un8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2LY4)