3I91 - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 8 (CBX8) WITH H3K9 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) - 06 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Chromobox Homolog 8, Cbx8, H3K9 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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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
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Chain A from PDB  Type:PROTEIN  Length:52
 aligned with CBX8_HUMAN | Q9HC52 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:52
                                    18        28        38        48        58  
            CBX8_HUMAN    9 RVFAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAFEER 60
               SCOP domains d3i91a_ A: automated matches                         SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CHROMO_2  PDB: A:11-60 UniProt: 11-69              PROSITE (1)
                PROSITE (2) -------------------CHROMO_1  PDB: A:28-4------------ PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                  3i91 A  9 RVFAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAFEER 60
                                    18        28        38        48        58

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with CBX8_HUMAN | Q9HC52 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:52
                                    18        28        38        48        58  
            CBX8_HUMAN    9 RVFAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAFEER 60
               SCOP domains d3i91b_ B: automated matches                         SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CHROMO_2  PDB: B:11-60 UniProt: 11-69              PROSITE (1)
                PROSITE (2) -------------------CHROMO_1  PDB: B:28-4------------ PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                  3i91 B  9 RVFAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAFEER 60
                                    18        28        38        48        58

Chain C from PDB  Type:PROTEIN  Length:8
                                       
               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
                  3i91 C  5 QTARkSTG 12
                                |   
                                9-M3L

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (21, 21)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CBX8_HUMAN | Q9HC52)

molecular function
	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).
	GO:0003727	single-stranded RNA binding	Interacting selectively and non-covalently with single-stranded RNA.
	GO:0097027	ubiquitin-protein transferase activator activity	Increases the activity of a ubiquitin-protein transferase, an enzyme that catalyzes the covalent attachment of ubiquitin to lysine in a substrate protein.
biological process
	GO:0070301	cellular response to hydrogen peroxide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
	GO:0016574	histone ubiquitination	The modification of histones by addition of ubiquitin groups.
	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:0045739	positive regulation of DNA repair	Any process that activates or increases the frequency, rate or extent of DNA repair.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0032967	positive regulation of collagen biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
	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:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	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: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: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.
	GO:0000151	ubiquitin ligase complex	A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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