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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 6 (CBX6) WITH H3K9 PEPTIDE
 
Authors :  A. Dong, M. F. Amaya, Z. Li, P. Loppnau, I. Kozieradzki, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, A. Bochkarev, J. Min, H. Ouya Structural Genomics Consortium (Sgc)
Date :  30 Mar 09  (Deposition) - 21 Apr 09  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chromobox Homolog, Cbx6, H3K9 Peptide, Sgc, Chromatin Regulator, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription Regulation, Chromosomal Protein, Dna-Binding, Nucleosome Core, Transcription-Dna Binding Protein Complex, Structural Genomics, Structural Genomics Consortium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Kaustov, H. Ouyang, M. Amaya, A. Lemak, N. Nady, S. Duan, G. A. Wasney Z. Li, M. Vedadi, M. Schapira, J. Min, C. H. Arrowsmith
Recognition And Specificity Determinants Of The Human Cbx Chromodomains.
J. Biol. Chem. V. 286 521 2011
PubMed-ID: 21047797  |  Reference-DOI: 10.1074/JBC.M110.191411

(-) Compounds

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 6
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P28A-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 8-65
    Gene: CBX6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HISTONE H3K9ME3 PEPTIDE
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 2-16
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN XENOPUS LAEVIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 3GV6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GV6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GV6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GV6)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX6_HUMAN11-69  1A:11-63
2CHROMO_1PS00598 Chromo domain signature.CBX6_HUMAN28-48  1A:28-48

(-) Exons   (0, 0)

(no "Exon" information available for 3GV6)

(-) Sequences/Alignments

Asymmetric/Biological 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:56
 aligned with CBX6_HUMAN | O95503 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:56
                                    17        27        37        47        57      
            CBX6_HUMAN    8 ERVFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKERE 63
               SCOP domains d3gv6a_ A: automated matches                             SCOP domains
               CATH domains 3gv6A00 A:8-63  [code=2.40.50.40, no name defined]       CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CHROMO_2  PDB: A:11-63 UniProt: 11-69                 PROSITE (1)
                PROSITE (2) --------------------CHROMO_1  PDB: A:28-4--------------- PROSITE (2)
                 Transcript -------------------------------------------------------- Transcript
                  3gv6 A  8 ERVFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKERE 63
                                    17        27        37        47        57      


Chain B from PDB  Type:PROTEIN  Length:6
 aligned with H32_XENLA | P84233 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:6
             H32_XENLA    6 QTARKS 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 ------ Transcript
                  3gv6 B  5 QTARkS 10
                                | 
                                9-M3L


Chain B from PDB  Type:PROTEIN  Length:6
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:6
          Q92133_XENLA    6 QTARKS 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 ------ Transcript
                  3gv6 B  5 QTARkS 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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GV6)

(-) Gene Ontology  (13, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBX6_HUMAN | O95503)
molecular function
    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:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
biological process
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0031519    PcG protein complex    A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
    GO:0000792    heterochromatin    A compact and highly condensed form of chromatin.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B   (Q92133_XENLA | Q92133)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
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: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.

Chain B   (H32_XENLA | P84233)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
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: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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  H32_XENLA | P84233
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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX6_HUMAN | O95503: 3i90
        H32_XENLA | P84233: 1f66 1kx3 1kx4 1kx5 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y
        Q92133_XENLA | Q92133: 2hue
UniProtKB/TrEMBL
        Q92133_XENLA | Q92133: 2l11 2l12 2l1b 3gl6 3h91 3me9 3mea 3met 3meu 3mev 3o7a 4hsu 4qeo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GV6)