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(-) Description

Title :  SOLUTION STRUCTURE OF THE ADD DOMAIN OF ATRX COMPLEXED WITH HISTONE TAIL H3 1-15 K9ME3
 
Authors :  S. Eustermann, J. Yang, D. Neuhaus
Date :  08 Apr 11  (Deposition) - 29 Jun 11  (Release) - 29 Jun 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,C  (25x)
NMR Structure *:  A,C  (1x)
Keywords :  Histone Tail, Metal Binding Protein-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Eustermann, J. Yang, M. J. Law, R. Amos, L. M. Chapman, C. Jelinska, D. Garrick, D. Clynes, R. J. Gibbons, D. Rhodes, D. R. Higgs, D. Neuhaus
Combinatorial Readout Of Histone H3 Modifications Specifies Localization Of Atrx To Heterochromatin
Nat. Struct. Mol. Biol. 2011
PubMed-ID: 21666677  |  Reference-DOI: 10.1038/NSMB.2070

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR ATRX
    ChainsA
    EC Number3.6.4.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET30A
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 159-296
    GeneATRX, RAD54L, XH2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATP-DEPENDENT HELICASE ATRX, X-LINKED HELICASE II, X-LINKED NUCLEAR PROTEIN, XNP, ZNF-HX
 
Molecule 2 - HISTONE TAIL H3 K9ME3
    ChainsC
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (25x)AC
NMR Structure * (1x)AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

NMR Structure (2, 4)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2ZN3Ligand/IonZINC ION
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
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

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (17, 17)

NMR Structure (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)
NMR Structure * (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)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_1PS00322 Histone H3 signature 1.H31_HUMAN15-21  1C:14-15
2ADDPS51533 ADD domain profile.ATRX_HUMAN159-296  1A:160-296
NMR Structure * (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_1PS00322 Histone H3 signature 1.H31_HUMAN15-21  1C:14-15
2ADDPS51533 ADD domain profile.ATRX_HUMAN159-296  1A:160-296

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003593032bENSE00001974165chr6:27858570-27858160411H31_HUMAN1-1361361C:1-1515

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:155-162 (gaps)19
2.9ENST000003733449ENSE00002165776X:76944420-76944311110ATRX_HUMAN162-198371A:163-19836
2.10ENST0000037334410ENSE00001694382X:76940498-7694043168ATRX_HUMAN199-221231A:199-22123
2.11bENST0000037334411bENSE00002071055X:76940085-769370123074ATRX_HUMAN221-124610261A:221-29676
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

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:142
 aligned with ATRX_HUMAN | P46100 from UniProtKB/Swiss-Prot  Length:2492

    Alignment length:154
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292    
           ATRX_HUMAN   143 GPEFRSRSKMKTENLKKRGEDGLHGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENLEQLLQQNKK 296
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----------.......-.......................eeee....eeeehhhhhhhhhh.....................eee......eeehhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh.... 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 ----------------ADD  PDB: A:160-296 UniProt: 159-296                                                                                                       PROSITE
           Transcript 2 (1) Exon 2.7a           ------------------------------------Exon 2.10              --------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) -------------------Exon 2.9  PDB: A:163-198 [INCOMPLETE]----------------------Exon 2.11b  PDB: A:221-296 UniProt: 221-1246 [INCOMPLETE]                    Transcript 2 (2)
                 2lbm A 155 G-----------AMADKRG-DGLHGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENLEQLLQQNKK 296
                            |        -  |     |-|      172       182       192       202       212       222       232       242       252       262       272       282       292    
                            |         156   162 |                                                                                                                                     
                          155                 163                                                                                                                                     

Chain C from PDB  Type:PROTEIN  Length:15
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:15
                                    11     
            H31_HUMAN     2 ARTKQTARKSTGGKA  16
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE -------------HI PROSITE
               Transcript 1 Exon 1.2b       Transcript 1
                 2lbm C   1 ARTKQTARkSTGGKA  15
                                    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 2LBM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (71, 79)

NMR Structure(hide GO term definitions)
Chain A   (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   (H31_HUMAN | P68431)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    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: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:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0060968    regulation of gene silencing    Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
    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.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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 2ld1 3ql9 3qla 3qlc 3qln 4w5a
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6

(-) Related Entries Specified in the PDB File

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