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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 6 (CBX6) WITH H3K27 PEPTIDE
 
Authors :  M. F. Amaya, M. Ravichandran, 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 :  10 Jul 09  (Deposition) - 08 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Chromobox Homolog 6, Cbx6, H3K27 Peptide, Structural Genomics, Structural Genomics Consortium, Sgc, Chromatin Regulator, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription Regulation (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, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-V2R-PRARE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CBX6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - H3K27 PEPTIDE
    Chains: C, D
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 3I90)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I90)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I90)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I90)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX6_HUMAN11-69
 		  2A:11-58
B:11-59
2CHROMO_1PS00598 Chromo domain signature.CBX6_HUMAN28-48
 		  2A:28-48
B:28-48
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX6_HUMAN11-69
 		  1A:11-58
-
2CHROMO_1PS00598 Chromo domain signature.CBX6_HUMAN28-48
 		  1A:28-48
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX6_HUMAN11-69
 		  1-
B:11-59
2CHROMO_1PS00598 Chromo domain signature.CBX6_HUMAN28-48
 		  1-
B:28-48

(-) Exons   (0, 0)

(no "Exon" information available for 3I90)

(-) 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:50
 aligned with CBX6_HUMAN | O95503 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:50
                                    18        28        38        48        58
            CBX6_HUMAN    9 RVFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFE 58
               SCOP domains d3i90a_ A: automated matches                       SCOP domains
               CATH domains 3i90A00 A:9-58  [code=2.40.50.40, no name defined] CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhh..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CHROMO_2  PDB: A:11-58 UniProt: 11-69            PROSITE (1)
                PROSITE (2) -------------------CHROMO_1  PDB: A:28-4---------- PROSITE (2)
                 Transcript -------------------------------------------------- Transcript
                  3i90 A  9 RVFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFE 58
                                    18        28        38        48        58


Chain B from PDB  Type:PROTEIN  Length:50
 aligned with CBX6_HUMAN | O95503 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:50
                                    19        29        39        49        59
            CBX6_HUMAN   10 VFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQ 59
               SCOP domains d3i90b_ B: automated matches                       SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeee...hhhhheeee.hhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CHROMO_2  PDB: B:11-59 UniProt: 11-69             PROSITE (1)
                PROSITE (2) ------------------CHROMO_1  PDB: B:28-4----------- PROSITE (2)
                 Transcript -------------------------------------------------- Transcript
                  3i90 B 10 VFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQ 59
                                    19        29        39        49        59


Chain C from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .....eee... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  3i90 C 19 QLATKAARkSA 29
                                    28 
                                   27-M3L


Chain D from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .....ee... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3i90 D 19 QLATKAARkS 28
                                    28
                                   27-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, 2)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I90)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX6_HUMAN | O95503: 3gv6

(-) Related Entries Specified in the PDB File

3i8y CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 2 (CBX2)IN COMPLEX WITH H3K27(ME)3 PEPTIDE
3i8z CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 4 (CBX4)
3i91 CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 8 (CBX8) WITH H3K9 PEPTIDE