3GS2 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   RING1B C-TERMINAL DOMAIN/CBX7 CBOX COMPLEX

Authors :   R. Wang, A. B. Taylor, C. A. Kim

Date :   26 Mar 09 (Deposition) - 25 Aug 10 (Release) - 25 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Ring1B, Cbox, Cbx7, Polycomb, E3-Ligase, Chromosomal Protein, Transcription Regulation, Chromatin Regulator, Transcription Repressor, Ligase, Metal-Binding, Nucleus, Phosphoprotein, Repressor, Transcription, Ubl Conjugation Pathway, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Wang, A. B. Taylor, B. Z. Leal, L. V. Chadwell, U. Ilangovan, A. K. Robinson, V. Schirf, P. J. Hart, E. M. Lafer, B. Demeler, A. P. Hinck, D. G. Mcewen, C. A. Kim
Polycomb Group Targeting Through Different Binding Partners Of Ring1B C-Terminal Domain.
Structure V. 18 966 2010
PubMed-ID: 20696397 | Reference-DOI: 10.1016/J.STR.2010.04.013

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE RING2
	Chains	:	A, C
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN, RESIDUES 223-333
	Gene	:	BAP1, DING, HIPI3, RING1B, RNF2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RING FINGER PROTEIN 2, RING FINGER PROTEIN 1B, RING1B, RING FINGER PROTEIN BAP-1, DING PROTEIN, HUNTINGTIN-INTERACTING PROTEIN 2- INTERACTING PROTEIN 3, HIP2-INTERACTING PROTEIN 3

Molecule 2 - CHROMOBOX PROTEIN HOMOLOG 7
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3C
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CBOX DOMAIN, RESIDUES 219-248
	Gene	:	CBX7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:54 , ARG A:266 , ARG A:273 , ARG C:273	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	ALA A:223 , HOH B:12 , HOH B:29 , HOH B:141 , ARG B:245 , ARG B:247	BINDING SITE FOR RESIDUE SO4 B 2
3	AC3	SOFTWARE	ALA A:223 , GLU A:312 , HOH B:29 , HOH B:141	BINDING SITE FOR RESIDUE ZN A 334

(no "SS Bond" information available for 3GS2)

Asymmetric Unit

No.	Residues
1	Ala C:298	-	Ser C:299

(no "SAP(SNP)/Variant" information available for 3GS2)

(no "PROSITE Motif" information available for 3GS2)

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000216133	1b	ENSE00001934950	chr22:39548655-39548381	275	CBX7_HUMAN	1-23	23	0	-	-
1.2a	ENST00000216133	2a	ENSE00000654689	chr22:39545837-39545794	44	CBX7_HUMAN	24-38	15	0	-	-
1.3a	ENST00000216133	3a	ENSE00001330607	chr22:39537441-39537376	66	CBX7_HUMAN	38-60	23	0	-	-
1.4	ENST00000216133	4	ENSE00001308314	chr22:39534707-39534641	67	CBX7_HUMAN	60-82	23	0	-	-
1.5c	ENST00000216133	5c	ENSE00000654684	chr22:39530757-39530406	352	CBX7_HUMAN	83-200	118	0	-	-
1.6b	ENST00000216133	6b	ENSE00001299764	chr22:39530053-39526777	3277	CBX7_HUMAN	200-251	52	2	B:219-248 D:219-247	30 29

2.1a	ENST00000367510	1a	ENSE00001030490	chr1:185014496-185014781	286	RING2_HUMAN	-	0	0	-	-
2.3	ENST00000367510	3	ENSE00002199249	chr1:185056684-185056772	89	RING2_HUMAN	1-29	29	0	-	-
2.4a	ENST00000367510	4a	ENSE00000822928	chr1:185060711-185060871	161	RING2_HUMAN	30-83	54	0	-	-
2.5	ENST00000367510	5	ENSE00000822929	chr1:185062193-185062408	216	RING2_HUMAN	83-155	73	0	-	-
2.6	ENST00000367510	6	ENSE00000822930	chr1:185067204-185067476	273	RING2_HUMAN	155-246	92	2	A:223-246 C:224-246	24 23
2.7b	ENST00000367510	7b	ENSE00000822931	chr1:185068923-185069094	172	RING2_HUMAN	246-303	58	2	A:246-303 (gaps) C:246-303 (gaps)	58 58
2.8b	ENST00000367510	8b	ENSE00001030494	chr1:185069332-185071740	2409	RING2_HUMAN	304-336	33	2	A:304-333 C:304-333	30 30

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:109
 aligned with RING2_HUMAN | Q99496 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:111
                                   232       242       252       262       272       282       292       302       312       322       332 
          RING2_HUMAN   223 ASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTK 333
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.............eeeeee...hhhhhhhhhhhhhhhhhhhhhhhh.......--...eeeeee.....eee.....hhhhhhhhhh.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.6  PDB: A:223-246---------------------------------------------------------Exon 2.8b  PDB: A:304-333      Transcript 2 (1)
           Transcript 2 (2) -----------------------Exon 2.7b  PDB: A:246-303 (gaps) UniProt: 246-303         ------------------------------ Transcript 2 (2)
                 3gs2 A 223 ASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDT--EKQYTIYIATASGQFTVLDGSFSLELVSEKYWKVNKPMELYYAPTK 333
                                   232       242       252       262       272       282  |  | 292       302       312       322       332 
                                                                                        285  |                                             
                                                                                           288

Chain B from PDB  Type:PROTEIN  Length:30
 aligned with CBX7_HUMAN | O95931 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:30
                                   228       238       248
           CBX7_HUMAN   219 EVTVTDITANSITVTFREAQAAEGFFRDRS 248
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
               Transcript 1 Exon 1.6b  PDB: B:219-248      Transcript 1
                 3gs2 B 219 EVTVTDITANSITVTFREAQAAEGFFRDRS 248
                                   228       238       248

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with RING2_HUMAN | Q99496 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:110
                                   233       243       253       263       273       283       293       303       313       323       333
          RING2_HUMAN   224 SEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTK 333
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.............eeeee....hhhhhhhhhhhhhhhhhhhhhhhh.......--...eeeeeee...eeee.....hhhhhhhhh......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.6  PDB: C:224-24---------------------------------------------------------Exon 2.8b  PDB: C:304-333      Transcript 2 (1)
           Transcript 2 (2) ----------------------Exon 2.7b  PDB: C:246-303 (gaps) UniProt: 246-303         ------------------------------ Transcript 2 (2)
                 3gs2 C 224 SEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDT--EKQYTIYIATASGQFTVLDGSFSLELVSEKYWKVNKPMELYYAPTK 333
                                   233       243       253       263       273       283 |  |  293       303       313       323       333
                                                                                       285  |                                             
                                                                                          288

Chain D from PDB  Type:PROTEIN  Length:29
 aligned with CBX7_HUMAN | O95931 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:29
                                   228       238         
           CBX7_HUMAN   219 EVTVTDITANSITVTFREAQAAEGFFRDR 247
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
               Transcript 1 Exon 1.6b  PDB: D:219-247     Transcript 1
                 3gs2 D 219 EVTVTDITANSITVTFREAQAAEGFFRDR 247
                                   228       238

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 '\|'

(no "SCOP Domain" information available for 3GS2)

(no "CATH Domain" information available for 3GS2)

(no "Pfam Domain" information available for 3GS2)

Asymmetric Unit(hide GO term definitions)

Chain A,C (RING2_HUMAN | Q99496)

molecular function
	GO:0071535	RING-like zinc finger domain binding	Interacting selectively and non-covalently with a RING-like zinc finger domain domain of a protein. The RING-like domain is a zinc finger domain that is related to the C3HC4 RING finger domain.
	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:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0009948	anterior/posterior axis specification	The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
	GO:0001702	gastrulation with mouth forming second	A gastrulation process in which the initial invagination becomes the anus and the mouth forms second.
	GO:0007281	germ cell development	The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
	GO:0035518	histone H2A monoubiquitination	The modification of histone H2A by addition of a single ubiquitin group.
	GO:0036353	histone H2A-K119 monoubiquitination	The modification of histone H2A by addition of a single ubiquitin group to lysine-119 (H2A- K119) in metazoans, and at the equivalent residue in other organisms.
	GO:0016574	histone ubiquitination	The modification of histones by addition of ubiquitin groups.
	GO:0000278	mitotic cell cycle	Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
	GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	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:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0032526	response to retinoic acid	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 retinoic acid stimulus.
	GO:0021510	spinal cord development	The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0071339	MLL1 complex	A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
	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:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000791	euchromatin	A dispersed and relatively uncompacted form of chromatin.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0016604	nuclear body	Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
	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:0001739	sex chromatin	Chromatin that is part of a sex chromosome.
	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.

Chain B,D (CBX7_HUMAN | O95931)

molecular function
	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).
	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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	RING2_HUMAN \| Q99496
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UniProtKB/Swiss-Prot
	CBX7_HUMAN \| O95931	:	2k1b 2l12 2l1b 4mn3 5epj
	RING2_HUMAN \| Q99496	:	2h0d 3h8h 3ixs 3rpg 4r8p 4s3o

(no "Related Entries Specified in the PDB File" available for 3GS2)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File