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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MACRO DOMAIN OF HUMAN CORE HISTONE H2A
 
Authors :  M. Vollmar, C. Phillips, E. P. Carpenter, J. R. C. Muniz, T. Krojer, E. Ugochukwu, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, O. Gileadi
Date :  29 Apr 10  (Deposition) - 19 May 10  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Chromosomal Protein, Nucleosome Core, Chromatin Regulator, Nucleus, Dna-Binding Protein, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Vollmar, C. Phillipps, E. P. Carpenter, J. R. C. Muniz, T. Krojer, E. Ugochukwu, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, O. Gileadi
Crystal Structure Of The Macro Domain Of Human Core Histone H2A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CORE HISTONE MACRO-H2A.2
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNH-TRXT
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentMACRO DOMAIN, RESIDUES 177-369
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTONE MACROH2A2, MH2A2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2XD7)

(-) Sites  (0, 0)

(no "Site" information available for 2XD7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XD7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:253 -Pro A:254
2Gly B:253 -Pro B:254
3Gly C:253 -Pro C:254
4Gly D:253 -Pro D:254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XD7)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.H2AW_HUMAN184-370
 
 
 
  4A:184-369
B:184-369
C:184-369
D:184-368
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.H2AW_HUMAN184-370
 
 
 
  1A:184-369
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.H2AW_HUMAN184-370
 
 
 
  1-
B:184-369
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.H2AW_HUMAN184-370
 
 
 
  1-
-
C:184-369
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.H2AW_HUMAN184-370
 
 
 
  1-
-
-
D:184-368

(-) Exons   (0, 0)

(no "Exon" information available for 2XD7)

(-) 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:192
 aligned with H2AW_HUMAN | Q9P0M6 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:192
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367  
           H2AW_HUMAN   178 GPGDGFTILSSKSLVLGQKLSLTQSDISHIGSMRVEGIVHPTTAEIDLKEDIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPKQTAAQVTLKAISAHFDDSSASSLKNVYFLLFDSESIGIYVQEMAKL 369
               SCOP domains d2xd7a_ A: automated matches                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee.....eeeeee.hhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------MACRO  PDB: A:184-369 UniProt: 184-370                                                                                                                                                     PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xd7 A 178 GPGDGFTILSSKSLVLGQKLSLTQSDISHIGSMRVEGIVHPTTAEIDLKEDIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPKQTAAQVTLKAISAHFDDSSASSLKNVYFLLFDSESIGIYVQEMAKL 369
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367  

Chain B from PDB  Type:PROTEIN  Length:192
 aligned with H2AW_HUMAN | Q9P0M6 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:192
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367  
           H2AW_HUMAN   178 GPGDGFTILSSKSLVLGQKLSLTQSDISHIGSMRVEGIVHPTTAEIDLKEDIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPKQTAAQVTLKAISAHFDDSSASSLKNVYFLLFDSESIGIYVQEMAKL 369
               SCOP domains d2xd7b_ B: automated matches                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee.....eeeeee.hhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------MACRO  PDB: B:184-369 UniProt: 184-370                                                                                                                                                     PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xd7 B 178 GPGDGFTILSSKSLVLGQKLSLTQSDISHIGSMRVEGIVHPTTAEIDLKEDIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPKQTAAQVTLKAISAHFDDSSASSLKNVYFLLFDSESIGIYVQEMAKL 369
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367  

Chain C from PDB  Type:PROTEIN  Length:193
 aligned with H2AW_HUMAN | Q9P0M6 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:193
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366   
           H2AW_HUMAN   177 DGPGDGFTILSSKSLVLGQKLSLTQSDISHIGSMRVEGIVHPTTAEIDLKEDIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPKQTAAQVTLKAISAHFDDSSASSLKNVYFLLFDSESIGIYVQEMAKL 369
               SCOP domains d2xd7c_ C: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee.....eeeeee.hhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------MACRO  PDB: C:184-369 UniProt: 184-370                                                                                                                                                     PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xd7 C 177 DGPGDGFTILSSKSLVLGQKLSLTQSDISHIGSMRVEGIVHPTTAEIDLKEDIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPKQTAAQVTLKAISAHFDDSSASSLKNVYFLLFDSESIGIYVQEMAKL 369
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366   

Chain D from PDB  Type:PROTEIN  Length:187
 aligned with H2AW_HUMAN | Q9P0M6 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:192
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  
           H2AW_HUMAN   177 DGPGDGFTILSSKSLVLGQKLSLTQSDISHIGSMRVEGIVHPTTAEIDLKEDIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPKQTAAQVTLKAISAHFDDSSASSLKNVYFLLFDSESIGIYVQEMAK 368
               SCOP domains d2xd7d_ D: automated matches                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------------Macro-2xd7D01 D:216-330                                                                                            -------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------Macro-2xd7D02 D:216-330                                                                                            -------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------Macro-2xd7D03 D:216-330                                                                                            -------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------Macro-2xd7D04 D:216-330                                                                                            -------------------------------------- Pfam domains (4)
         Sec.struct. author .......eeeeeee.....eeeeee.hhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeee....-----.hhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------MACRO  PDB: D:184-368 UniProt: 184-370                                                                                                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xd7 D 177 DGPGDGFTILSSKSLVLGQKLSLTQSDISHIGSMRVEGIVHPTTAEIDLKEDIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFP-----FPKQTAAQVTLKAISAHFDDSSASSLKNVYFLLFDSESIGIYVQEMAK 368
                                   186       196       206       216       226       236       246       256       266       276       286       296       306        |-    |  326       336       346       356       366  
                                                                                                                                                                    315   321                                               

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XD7)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: MACRO (14)
1aMacro-2xd7D01D:216-330
1bMacro-2xd7D02D:216-330
1cMacro-2xd7D03D:216-330
1dMacro-2xd7D04D:216-330

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (H2AW_HUMAN | Q9P0M6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0031490    chromatin DNA binding    Interacting selectively and non-covalently with DNA that is assembled into chromatin.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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.
biological process
    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:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    GO:0007549    dosage compensation    Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes.
    GO:0071169    establishment of protein localization to chromatin    The directed movement of a protein to a part of a chromosome that is organized into chromatin.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    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:1901837    negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter    Any process that stops, prevents or reduces the frequency, rate or extent of transcription of nuclear large rRNA transcript from RNA polymerase I 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:0045618    positive regulation of keratinocyte differentiation    Any process that activates or increases the frequency, rate or extent of keratinocyte differentiation.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
cellular component
    GO:0001740    Barr body    A structure found in a female mammalian cell containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery.
    GO:0035098    ESC/E(Z) complex    A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4.
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    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:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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.

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