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(-) Description

Title :  SOLUTION STRUCTURE OF THE CBX7 CHROMODOMAIN IN COMPLEX WITH A H3K27ME2 PEPTIDE
 
Authors :  K. L. Yap, L. Zeng, M. Zhou
Date :  17 Mar 10  (Deposition) - 30 Jun 10  (Release) - 30 Jun 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Histone Modification, Lysine Methylation, Chromobox, Polycomb, Chromatin-Binding, Chromatin Regulator, Nucleus, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Yap, S. Li, A. M. Munoz-Cabello, S. Raguz, L. Zeng, S. Mujtaba, J. Gil, M. J. Walsh, M. M. Zhou
Molecular Interplay Of The Noncoding Rna Anril And Methylated Histone H3 Lysine 27 By Polycomb Cbx7 In Transcriptional Silencing Of Ink4A.
Mol. Cell V. 38 662 2010
PubMed-ID: 20541999  |  Reference-DOI: 10.1016/J.MOLCEL.2010.03.021

(-) Compounds

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 7
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CHROMODOMAIN
    Gene: CBX7, D15ERTD417E
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - HISTONE H3 PEPTIDE (RESIDUES 15-30) WITH DIMETHYLATED LYSINE 27
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 2KVM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX7_MOUSE11-69  1A:11-69
2CHROMO_1PS00598 Chromo domain signature.CBX7_MOUSE28-48  1A:28-48
NMR Structure * (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX7_MOUSE11-69  1A:11-69
2CHROMO_1PS00598 Chromo domain signature.CBX7_MOUSE28-48  1A:28-48

(-) Exons   (0, 0)

(no "Exon" information available for 2KVM)

(-) 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:71
 aligned with CBX7_MOUSE | Q8VDS3 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:71
                                    10        20        30        40        50        60        70 
            CBX7_MOUSE    1 MELSAIGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERDRASGYRK 71
               SCOP domains d2kvma_ A: automated matches                                            SCOP domains
               CATH domains 2kvmA00 A:1-71  [code=2.40.50.40, no name defined]                      CATH domains
               Pfam domains ----------Chromo-2kvmA01 A:11-60                            ----------- Pfam domains
         Sec.struct. author ............eeeeeeeeee..eeeeeeee...hhhhheeee.....hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------CHROMO_2  PDB: A:11-69 UniProt: 11-69                      -- PROSITE (1)
                PROSITE (2) ---------------------------CHROMO_1  PDB: A:28-4----------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------- Transcript
                  2kvm A  1 MELSAIGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERDRASGYRK 71
                                    10        20        30        40        50        60        70 


Chain B from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ................ Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2kvm B 15 APRKQLATKAARkSAP 30
                                    24  |   
                                       27-MLY
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Tudor (88)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (CBX7_MOUSE | Q8VDS3)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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: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:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0048733    sebaceous gland development    The process whose specific outcome is the progression of the sebaceous gland over time, from its formation to the mature structure.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0035102    PRC1 complex    A multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000792    heterochromatin    A compact and highly condensed form of chromatin.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.

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  2kvm
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  CBX7_MOUSE | Q8VDS3
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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX7_MOUSE | Q8VDS3: 4x3k 4x3s 4x3t 4x3u 5ejw

(-) Related Entries Specified in the PDB File

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