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(-) Description

Title :  SOLUTION STRUCTURE OF THE CHROMO DOMAIN OF CHROMOBOX HOMOLOG 2 FROM HUMAN
 
Authors :  H. Li, K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Dec 05  (Deposition) - 02 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Chromobox Homolog 2, Chromo Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Li, K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Chromo Domain Of Chromobox Homolog 2 From Human
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 2 (ISOFORM 2)
    ChainsA
    EngineeredYES
    Expression System PlasmidP050613-29
    Expression System Vector TypePLASMID
    FragmentCHROMO DOMAIN
    GeneCBX2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2D9U)

(-) Sites  (0, 0)

(no "Site" information available for 2D9U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D9U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D9U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D9U)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX2_HUMAN12-70  1A:11-68
2CHROMO_1PS00598 Chromo domain signature.CBX2_HUMAN29-49  1A:28-48

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003109421ENSE00001241976chr17:77751993-77752106114CBX2_HUMAN1-24241A:1-2323
1.2ENST000003109422ENSE00001164309chr17:77752183-7775222644CBX2_HUMAN25-39151A:24-3815
1.3ENST000003109423ENSE00000949912chr17:77753161-7775322666CBX2_HUMAN39-61231A:38-6023
1.4aENST000003109424aENSE00001465034chr17:77755495-77755600106CBX2_HUMAN61-96361A:60-689
1.5ENST000003109425ENSE00001193142chr17:77757531-777613783848CBX2_HUMAN97-5324361A:69-746

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:74
 aligned with CBX2_HUMAN | Q14781 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:110
                                    11        21        31        41        51        61        71        81        91       101       111
           CBX2_HUMAN     2 EELSSVGEQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQKKEHEKEVQNRKRGKRPRGRPRKLTAMSSCSRRSKLKEPDAPSKSKSSSSSS 111
               SCOP domains d2d9ua_ A: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee..eeeeeeee........eeeehhh...hhhhhhhhhhhhhh....------------------------------------...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------CHROMO_2  PDB: A:11-68 UniProt: 12-70                      ----------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------CHROMO_1  PDB: A:28-4-------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:1-23  Exon 1.2       ---------------------Exon 1.4a  PDB: A:60-68 [INCOMPLETE]Exon 1.5        Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.3  PDB: A:38-60 -------------------------------------------------- Transcript 1 (2)
                 2d9u A   1 GSSGSSGEQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQKKEHEKEVQN------------------------------------SGPSSG  74
                                    10        20        30        40        50        60       | -         -         -         -    |   74
                                                                                              68                                   69     

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D9U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D9U)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (CBX2_HUMAN | Q14781)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0045137    development of primary sexual characteristics    The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion.
    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:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007548    sex differentiation    The establishment of the sex of an organism by physical differentiation.
    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:0000791    euchromatin    A dispersed and relatively uncompacted form of chromatin.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX2_HUMAN | Q147813h91 5epk

(-) Related Entries Specified in the PDB File

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