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(-) Description

Title :  HEXAGONAL COMPLEX STRUCTURE OF ATRX ADD BOUND TO H3K9ME3 PEPTIDE
 
Authors :  B. Xiang, H. Li
Date :  02 Feb 11  (Deposition) - 15 Jun 11  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,C,D,F
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  D,F  (1x)
Keywords :  Zinc Finger, Transcription, Histone, Lysine Trimethylation, Nuclear Protein, Histone-Binding Protein, Transcription-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Iwase, B. Xiang, S. Ghosh, T. Ren, P. W. Lewis, J. C. Cochrane, C. D. Allis, D. J. Picketts, D. J. Patel, H. Li, Y. Shi
Atrx Add Domain Links An Atypical Histone Methylation Recognition Mechanism To Human Mental-Retardation Syndrome
Nat. Struct. Mol. Biol. V. 18 769 2011
PubMed-ID: 21666679  |  Reference-DOI: 10.1038/NSMB.2062

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR ATRX
    ChainsA, D
    EC Number3.6.4.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P
    Expression System StrainROSETTA 2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL ADD DOMAIN, UNP RESIDUES 167-289
    GeneATRX, RAD54L, XH2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATP-DEPENDENT HELICASE ATRX, X-LINKED HELICASE II, X-LINKED NUCLEAR PROTEIN, XNP, ZNF-HX
 
Molecule 2 - PEPTIDE OF HISTONE H3.3
    ChainsC, F
    EngineeredYES
    FragmentN-TERMINAL TAIL, UNP RESIDUES 2-16
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ACDF
Biological Unit 1 (1x)AC  
Biological Unit 2 (1x)  DF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:171 , CYS A:174 , CYS A:197 , CYS A:200BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS A:220 , CYS A:223 , CYS A:240 , CYS A:243BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWARECYS A:232 , CYS A:235 , CYS A:265 , CYS A:268BINDING SITE FOR RESIDUE ZN A 3
4AC4SOFTWARELYS A:183 , ILE A:186 , TYR A:187 , HOH D:109 , MET D:205 , SER D:206 , HOH D:453BINDING SITE FOR RESIDUE K A 290
5AC5SOFTWARECYS D:171 , CYS D:174 , CYS D:197 , CYS D:200BINDING SITE FOR RESIDUE ZN D 1
6AC6SOFTWARECYS D:220 , CYS D:223 , CYS D:240 , CYS D:243BINDING SITE FOR RESIDUE ZN D 2
7AC7SOFTWARECYS D:232 , CYS D:235 , CYS D:265 , CYS D:268BINDING SITE FOR RESIDUE ZN D 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QLA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QLA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (17, 34)

Asymmetric Unit (17, 34)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_012113G175EATRX_HUMANDisease (ATRX)  ---A/DG175E
02UniProtVAR_012115N179SATRX_HUMANDisease (ATRX)  ---A/DN179S
03UniProtVAR_001226P190AATRX_HUMANDisease (ATRX)  ---A/DP190A
04UniProtVAR_012116P190LATRX_HUMANDisease (ATRX)  ---A/DP190L
05UniProtVAR_012117P190SATRX_HUMANDisease (ATRX)  ---A/DP190S
06UniProtVAR_001227L192FATRX_HUMANDisease (ATRX)  ---A/DL192F
07UniProtVAR_012118V194IATRX_HUMANDisease (ATRX)  ---A/DV194I
08UniProtVAR_001228C200SATRX_HUMANDisease (ATRX)  ---A/DC200S
09UniProtVAR_012119Q219PATRX_HUMANDisease (ATRX)  ---A/DQ219P
10UniProtVAR_001229C220RATRX_HUMANDisease (ATRX)  ---A/DC220R
11UniProtVAR_032625C220YATRX_HUMANDisease (MRXSHF1)  ---A/DC220Y
12UniProtVAR_001230W222SATRX_HUMANDisease (ATRX)  ---A/DW222S
13UniProtVAR_001231C243FATRX_HUMANDisease (ATRX)  ---A/DC243F
14UniProtVAR_001232R246CATRX_HUMANDisease (ATRX)  ---A/DR246C
15UniProtVAR_010914R246LATRX_HUMANDisease (ATRX)  ---A/DR246L
16UniProtVAR_012120G249CATRX_HUMANDisease (ATRX)  ---A/DG249C
17UniProtVAR_001233G249DATRX_HUMANDisease (ATRX)  ---A/DG249D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (17, 17)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_012113G175EATRX_HUMANDisease (ATRX)  ---AG175E
02UniProtVAR_012115N179SATRX_HUMANDisease (ATRX)  ---AN179S
03UniProtVAR_001226P190AATRX_HUMANDisease (ATRX)  ---AP190A
04UniProtVAR_012116P190LATRX_HUMANDisease (ATRX)  ---AP190L
05UniProtVAR_012117P190SATRX_HUMANDisease (ATRX)  ---AP190S
06UniProtVAR_001227L192FATRX_HUMANDisease (ATRX)  ---AL192F
07UniProtVAR_012118V194IATRX_HUMANDisease (ATRX)  ---AV194I
08UniProtVAR_001228C200SATRX_HUMANDisease (ATRX)  ---AC200S
09UniProtVAR_012119Q219PATRX_HUMANDisease (ATRX)  ---AQ219P
10UniProtVAR_001229C220RATRX_HUMANDisease (ATRX)  ---AC220R
11UniProtVAR_032625C220YATRX_HUMANDisease (MRXSHF1)  ---AC220Y
12UniProtVAR_001230W222SATRX_HUMANDisease (ATRX)  ---AW222S
13UniProtVAR_001231C243FATRX_HUMANDisease (ATRX)  ---AC243F
14UniProtVAR_001232R246CATRX_HUMANDisease (ATRX)  ---AR246C
15UniProtVAR_010914R246LATRX_HUMANDisease (ATRX)  ---AR246L
16UniProtVAR_012120G249CATRX_HUMANDisease (ATRX)  ---AG249C
17UniProtVAR_001233G249DATRX_HUMANDisease (ATRX)  ---AG249D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (17, 17)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_012113G175EATRX_HUMANDisease (ATRX)  ---DG175E
02UniProtVAR_012115N179SATRX_HUMANDisease (ATRX)  ---DN179S
03UniProtVAR_001226P190AATRX_HUMANDisease (ATRX)  ---DP190A
04UniProtVAR_012116P190LATRX_HUMANDisease (ATRX)  ---DP190L
05UniProtVAR_012117P190SATRX_HUMANDisease (ATRX)  ---DP190S
06UniProtVAR_001227L192FATRX_HUMANDisease (ATRX)  ---DL192F
07UniProtVAR_012118V194IATRX_HUMANDisease (ATRX)  ---DV194I
08UniProtVAR_001228C200SATRX_HUMANDisease (ATRX)  ---DC200S
09UniProtVAR_012119Q219PATRX_HUMANDisease (ATRX)  ---DQ219P
10UniProtVAR_001229C220RATRX_HUMANDisease (ATRX)  ---DC220R
11UniProtVAR_032625C220YATRX_HUMANDisease (MRXSHF1)  ---DC220Y
12UniProtVAR_001230W222SATRX_HUMANDisease (ATRX)  ---DW222S
13UniProtVAR_001231C243FATRX_HUMANDisease (ATRX)  ---DC243F
14UniProtVAR_001232R246CATRX_HUMANDisease (ATRX)  ---DR246C
15UniProtVAR_010914R246LATRX_HUMANDisease (ATRX)  ---DR246L
16UniProtVAR_012120G249CATRX_HUMANDisease (ATRX)  ---DG249C
17UniProtVAR_001233G249DATRX_HUMANDisease (ATRX)  ---DG249D

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QLA)

(-) Exons   (5, 9)

Asymmetric Unit (5, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003668161ENSE00001442675chr1:226249552-226249795244H33_HUMAN-00--
1.2cENST000003668162cENSE00001442674chr1:226250436-22625051277H33_HUMAN-00--
1.3bENST000003668163bENSE00001428176chr1:226252030-226252180151H33_HUMAN1-43432C:1-10
F:1-10
10
10
1.4aENST000003668164aENSE00001692850chr1:226253357-226253510154H33_HUMAN43-94520--
1.5aENST000003668165aENSE00001381318chr1:226259052-226259224173H33_HUMAN95-136420--

2.1aENST000003733441aENSE00002167359X:77041702-77041468235ATRX_HUMAN1-770--
2.2ENST000003733442ENSE00001636919X:76972720-76972608113ATRX_HUMAN7-45390--
2.4bENST000003733444bENSE00001688675X:76954117-7695406256ATRX_HUMAN45-63190--
2.5ENST000003733445ENSE00001763951X:76953123-7695307153ATRX_HUMAN64-81180--
2.6ENST000003733446ENSE00001652735X:76952192-76952065128ATRX_HUMAN81-124440--
2.7aENST000003733447aENSE00002168990X:76949426-76949313114ATRX_HUMAN124-162391A:161-162
-
2
-
2.9ENST000003733449ENSE00002165776X:76944420-76944311110ATRX_HUMAN162-198372A:162-198
D:169-198
37
30
2.10ENST0000037334410ENSE00001694382X:76940498-7694043168ATRX_HUMAN199-221232A:199-221
D:199-221
23
23
2.11bENST0000037334411bENSE00002071055X:76940085-769370123074ATRX_HUMAN221-124610262A:221-287
D:221-287
67
67
2.12aENST0000037334412aENSE00001638399X:76931793-7693172173ATRX_HUMAN1246-1270250--
2.13ENST0000037334413ENSE00001655114X:76920267-76920134134ATRX_HUMAN1270-1315460--
2.14ENST0000037334414ENSE00001618412X:76919047-76918871177ATRX_HUMAN1315-1374600--
2.15ENST0000037334415ENSE00001759922X:76912143-7691205094ATRX_HUMAN1374-1405320--
2.16ENST0000037334416ENSE00002155398X:76909690-76909588103ATRX_HUMAN1405-1439350--
2.17ENST0000037334417ENSE00001804555X:76907843-76907604240ATRX_HUMAN1440-1519800--
2.18ENST0000037334418ENSE00001692523X:76891547-76891406142ATRX_HUMAN1520-1567480--
2.19aENST0000037334419aENSE00001634558X:76890194-76890085110ATRX_HUMAN1567-1603370--
2.20aENST0000037334420aENSE00001729307X:76889200-76889054147ATRX_HUMAN1604-1652490--
2.21ENST0000037334421ENSE00001679104X:76888872-76888695178ATRX_HUMAN1653-1712600--
2.22ENST0000037334422ENSE00001611054X:76876000-76875863138ATRX_HUMAN1712-1758470--
2.23ENST0000037334423ENSE00001600235X:76874449-76874274176ATRX_HUMAN1758-1816590--
2.24ENST0000037334424ENSE00001614801X:76872198-76872081118ATRX_HUMAN1817-1856400--
2.26bENST0000037334426bENSE00001611019X:76856033-76855903131ATRX_HUMAN1856-1899440--
2.27bENST0000037334427bENSE00001762228X:76855289-7685520189ATRX_HUMAN1900-1929300--
2.28ENST0000037334428ENSE00001627804X:76855049-76854880170ATRX_HUMAN1929-1986580--
2.29ENST0000037334429ENSE00001690714X:76849319-76849166154ATRX_HUMAN1986-2037520--
2.30ENST0000037334430ENSE00001637691X:76845410-76845304107ATRX_HUMAN2037-2073370--
2.31ENST0000037334431ENSE00001632927X:76829823-76829715109ATRX_HUMAN2073-2109370--
2.32ENST0000037334432ENSE00001674842X:76814317-76814140178ATRX_HUMAN2109-2168600--
2.33ENST0000037334433ENSE00001762255X:76813116-76812922195ATRX_HUMAN2169-2233650--
2.34ENST0000037334434ENSE00001605899X:76778879-76778730150ATRX_HUMAN2234-2283500--
2.35ENST0000037334435ENSE00001640278X:76777866-76777741126ATRX_HUMAN2284-2325420--
2.36ENST0000037334436ENSE00001609746X:76776976-7677688196ATRX_HUMAN2326-2357320--
2.37ENST0000037334437ENSE00001620267X:76776394-76776266129ATRX_HUMAN2358-2400430--
2.38ENST0000037334438ENSE00001885562X:76764107-767603783730ATRX_HUMAN2401-2492920--

(-) Sequences/Alignments

Asymmetric Unit
   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:127
 aligned with ATRX_HUMAN | P46100 from UniProtKB/Swiss-Prot  Length:2492

    Alignment length:127
                                   170       180       190       200       210       220       230       240       250       260       270       280       
           ATRX_HUMAN   161 GEDGLHGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENL 287
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhh.eee......eeehhhhhhhhhh....................eeee......eeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) --------------E---S----------A-F-I-----S------------------PR-S--------------------F--C--C-------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------L-----------------------------Y-------------------------L--D-------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -----------------------------S------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) 2.------------------------------------Exon 2.10              ------------------------------------------------------------------ Transcript 2 (1)
           Transcript 2 (2) -Exon 2.9  PDB: A:162-198             ----------------------Exon 2.11b  PDB: A:221-287 UniProt: 221-1246 [INCOMPLETE]           Transcript 2 (2)
                 3qla A 161 GPLGSMGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPLLDLVTACNSVYENL 287
                                   170       180       190       200       210       220       230       240       250       260       270       280       

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with H33_HUMAN | P84243 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:10
                                    11
            H33_HUMAN     2 ARTKQTARKS  11
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..eee..... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
               Transcript 1 Exon 1.3b  Transcript 1
                 3qla C   1 ARTKQTARkS  10
                                    10
                                    9-M3L

Chain D from PDB  Type:PROTEIN  Length:119
 aligned with ATRX_HUMAN | P46100 from UniProtKB/Swiss-Prot  Length:2492

    Alignment length:119
                                   178       188       198       208       218       228       238       248       258       268       278         
           ATRX_HUMAN   169 VSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENL 287
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhee......eehhhhhhhhhhh....................eeee......eeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ------E---S----------A-F-I-----S------------------PR-S--------------------F--C--C-------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------L-----------------------------Y-------------------------L--D-------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------S------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) ------------------------------Exon 2.10              ------------------------------------------------------------------ Transcript 2 (1)
           Transcript 2 (2) Exon 2.9  PDB: D:169-198      ----------------------Exon 2.11b  PDB: D:221-287 UniProt: 221-1246 [INCOMPLETE]           Transcript 2 (2)
                 3qla D 169 VSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPLLDLVTACNSVYENL 287
                                   178       188       198       208       218       228       238       248       258       268       278         

Chain F from PDB  Type:PROTEIN  Length:10
 aligned with H33_HUMAN | P84243 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:10
                                    11
            H33_HUMAN     2 ARTKQTARKS  11
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eeee..... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
               Transcript 1 Exon 1.3b  Transcript 1
                 3qla F   1 ARTKQTARkS  10
                                    10
                                    9-M3L

   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  (0, 0)

(no "SCOP Domain" information available for 3QLA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QLA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QLA)

(-) Gene Ontology  (71, 80)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (ATRX_HUMAN | P46100)
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:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0015616    DNA translocase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.
    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:0070087    chromo shadow domain binding    Interacting selectively and non-covalently with a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
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:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    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:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    GO:0060009    Sertoli cell development    The process whose specific outcome is the progression of a Sertoli cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a Sertoli cell fate.
    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:0072711    cellular response to hydroxyurea    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 hydroxyurea stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:1904908    negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric    Any process that stops, prevents or reduces the frequency, rate or extent of maintenance of mitotic sister chromatid cohesion, telomeric.
    GO:1901581    negative regulation of telomeric RNA transcription from RNA pol II promoter    Any process that stops, prevents or reduces the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0010571    positive regulation of nuclear cell cycle DNA replication    Any process that activates or increases the frequency, rate or extent of The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle.
    GO:0032206    positive regulation of telomere maintenance    Any process that activates or increases the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:1901582    positive regulation of telomeric RNA transcription from RNA pol II promoter    Any process that activates or increases the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
    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:0035128    post-embryonic forelimb morphogenesis    The process, occurring after embryonic development, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an organism.
    GO:0070198    protein localization to chromosome, telomeric region    Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0031297    replication fork processing    The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
    GO:0072520    seminiferous tubule development    The reproductive developmental process whose specific outcome is the progression of the seminiferous tubule over time, from its formation to the mature structure. Seminiferous tubules are ducts located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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:0070603    SWI/SNF superfamily-type complex    A protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the core components and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000792    heterochromatin    A compact and highly condensed form of chromatin.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    GO:1990707    nuclear subtelomeric heterochromatin    Heterochromatic regions of the chromosome found at the subtelomeric regions of a chromosome in the nucleus.
    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:0005721    pericentric heterochromatin    Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    GO:0031933    telomeric heterochromatin    Heterochromatic regions of the chromosome found at the telomeres.

Chain C,F   (H33_HUMAN | P84243)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000979    RNA polymerase II core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    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.
biological process
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0009725    response to hormone    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 hormone stimulus.
    GO:0032200    telomere organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000788    nuclear nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ATRX_HUMAN | P461002jm1 2lbm 2ld1 3ql9 3qlc 3qln 4w5a
        H33_HUMAN | P842431pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qlc 3wtp 4gne 4gnf 4gng 4gu0 4gur 4gus 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4tmp 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5ja4 5jjy 5jlb 5kdm 5x7x

(-) Related Entries Specified in the PDB File

3ql9 SAME COMPLEX, MONOCLINIC CRYSTAL FORM
3qlc THE SAME PROTEIN COMPLEXED WITH UNMODIFIED H3(1-15) PEPTIDE
3qln ATRX ADD DOMAIN IN FREE STATE