3H91 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN CHROMOBOX HOMOLOG 2 (CBX2) AND 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 :   29 Apr 09 (Deposition) - 18 Aug 09 (Release) - 06 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (2x)
Biol. Unit 2: A,C  (1x)
Biol. Unit 3: B,D  (2x)
Biol. Unit 4: B,D  (1x)

Keywords :   Human Chromobox Homolog 2, Cbx2, H3K27, Structural Genomics, Structural Genomics Consortium, Sgc, Chromatin Regulator, Dna- Binding, Nucleus, 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

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 9-62
	Gene	:	CBX2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - H3K27 PEPTIDE
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A		C
Biological Unit 2 (1x)	:	A		C
Biological Unit 3 (2x)	:		B		D
Biological Unit 4 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	M3L	2	Mod. Amino Acid	N-TRIMETHYLLYSINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	M3L	2	Mod. Amino Acid	N-TRIMETHYLLYSINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	M3L	2	Mod. Amino Acid	N-TRIMETHYLLYSINE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE

(no "Site" information available for 3H91)

Asymmetric Unit

No.	Residues
1	A:16	-	A:16
2	B:16	-	B:16

(no "Cis Peptide Bond" information available for 3H91)

(no "SAP(SNP)/Variant" information available for 3H91)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX2_HUMAN	12-70	2	A:12-60 B:12-60
2	CHROMO_1	PS00598	Chromo domain signature.	CBX2_HUMAN	29-49	2	A:29-49 B:29-49

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX2_HUMAN	12-70	2	A:12-60 -
2	CHROMO_1	PS00598	Chromo domain signature.	CBX2_HUMAN	29-49	2	A:29-49 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX2_HUMAN	12-70	1	A:12-60 -
2	CHROMO_1	PS00598	Chromo domain signature.	CBX2_HUMAN	29-49	1	A:29-49 -

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX2_HUMAN	12-70	2	- B:12-60
2	CHROMO_1	PS00598	Chromo domain signature.	CBX2_HUMAN	29-49	2	- B:29-49

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX2_HUMAN	12-70	1	- B:12-60
2	CHROMO_1	PS00598	Chromo domain signature.	CBX2_HUMAN	29-49	1	- B:29-49

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000310942	1	ENSE00001241976	chr17:77751993-77752106	114	CBX2_HUMAN	1-24	24	2	A:9-24 B:9-24	16 16
1.2	ENST00000310942	2	ENSE00001164309	chr17:77752183-77752226	44	CBX2_HUMAN	25-39	15	2	A:25-39 B:25-39	15 15
1.3	ENST00000310942	3	ENSE00000949912	chr17:77753161-77753226	66	CBX2_HUMAN	39-61	23	2	A:39-60 B:39-60	22 22
1.4a	ENST00000310942	4a	ENSE00001465034	chr17:77755495-77755600	106	CBX2_HUMAN	61-96	36	0	-	-
1.5	ENST00000310942	5	ENSE00001193142	chr17:77757531-77761378	3848	CBX2_HUMAN	97-532	436	0	-	-

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:52
 aligned with CBX2_HUMAN | Q14781 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:52
                                    18        28        38        48        58  
            CBX2_HUMAN    9 EQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQK 60
               SCOP domains d3h91a_ A: automated matches                         SCOP domains
               CATH domains 3h91A00 A:9-60  [code=2.40.50.40, no name defined]   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CHROMO_2  PDB: A:12-60 UniProt: 12-70             PROSITE (1)
                PROSITE (2) --------------------CHROMO_1  PDB: A:29-4----------- PROSITE (2)
           Transcript 1 (1) Exon 1.1        Exon 1.2       --------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: A:39-60 Transcript 1 (2)
                  3h91 A  9 EQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQK 60
                                    18        28        38        48        58

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with CBX2_HUMAN | Q14781 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:52
                                    18        28        38        48        58  
            CBX2_HUMAN    9 EQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQK 60
               SCOP domains d3h91b_ B: automated matches                         SCOP domains
               CATH domains 3h91B00 B:9-60  [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: B:12-60 UniProt: 12-70             PROSITE (1)
                PROSITE (2) --------------------CHROMO_1  PDB: B:29-4----------- PROSITE (2)
           Transcript 1 (1) Exon 1.1        Exon 1.2       --------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: B:39-60 Transcript 1 (2)
                  3h91 B  9 EQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQK 60
                                    18        28        38        48        58

Chain C from PDB  Type:PROTEIN  Length:9
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:9
          Q92133_XENLA   21 LATKAARKS 29
               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
                  3h91 C 20 LATKAARkS 28
                                   | 
                                  27-M3L

Chain D from PDB  Type:PROTEIN  Length:9
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:9
          Q92133_XENLA   21 LATKAARKS 29
               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
                  3h91 D 20 LATKAARkS 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Chromo domain-like (82)

Family: Chromo domain (41)

Protein domain: automated matches (12)

Human (Homo sapiens) [TaxId: 9606] (11)

1a	d3h91a_	A:
1b	d3h91b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.40, no name defined] (161)

Human (Homo sapiens) (86)

1a	3h91A00	A:9-60
1b	3h91B00	B:9-60

(no "Pfam Domain" information available for 3H91)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Chain C,D (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.

Asymmetric Unit
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(no "Sites" information available for 3h91)

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(no "Cis Peptide Bonds" information available for 3h91)

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	3h91
		Family and Domain Information	:	ProDom \| SYSTERS
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	CBX2_HUMAN \| Q14781
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	Q92133_XENLA \| Q92133
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UniProtKB/Swiss-Prot
	CBX2_HUMAN \| Q14781	:	2d9u 5epk
	Q92133_XENLA \| Q92133	:	2hue 3gv6
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	Q92133_XENLA \| Q92133	:	2l11 2l12 2l1b 3gl6 3me9 3mea 3met 3meu 3mev 3o7a 4hsu 4qeo

(no "Related Entries Specified in the PDB File" available for 3H91)

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (2, 2)

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Exons (3, 6)

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