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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION NMR STRUCTURE OF THE CHROMOBOX PROTEIN CBX7 WITH H3K27ME3

Authors :   L. Kaustov, A. Lemak, C. Fares, A. Gutmanas, R. Muhandiram, H. Quang, P. J. Min, A. Edwards, C. Arrowsmith

Date :   27 Jul 10 (Deposition) - 25 Aug 10 (Release) - 06 Apr 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Chromodomain, Structural Genomics, Structural Genomics Consortium, Sgc, Transcription Regulator (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 7
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3) CODON PLUS RIL
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A-MHL
	Fragment	:	UNP RESIDUES 7-62
	Gene	:	CBX7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Strain	:	BL21(DE3) CODON PLUS RIL (STRATAGENE)

Molecule 2 - HISTONE H3
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 20-34
	Organism Common	:	CLAWED FROG,COMMON PLATANNA,PLATANNA
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Other Details	:	H3K27ME3 15-MER PEPTIDE
	Synthetic	:	YES

		1	2
NMR Structure (20x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

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

NMR Structure * (1, 1)

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

(no "Site" information available for 2L1B)

(no "SS Bond" information available for 2L1B)

(no "Cis Peptide Bond" information available for 2L1B)

(no "SAP(SNP)/Variant" information available for 2L1B)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX7_HUMAN	11-69	1	A:5-56
2	CHROMO_1	PS00598	Chromo domain signature.	CBX7_HUMAN	28-48	1	A:22-42

NMR Structure * (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX7_HUMAN	11-69	1	A:5-56
2	CHROMO_1	PS00598	Chromo domain signature.	CBX7_HUMAN	28-48	1	A:22-42

NMR Structure (4, 4)

	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	1	A:1-17	17
1.2a	ENST00000216133	2a	ENSE00000654689	chr22:39545837-39545794	44	CBX7_HUMAN	24-38	15	1	A:18-32	15
1.3a	ENST00000216133	3a	ENSE00001330607	chr22:39537441-39537376	66	CBX7_HUMAN	38-60	23	1	A:32-54	23
1.4	ENST00000216133	4	ENSE00001308314	chr22:39534707-39534641	67	CBX7_HUMAN	60-82	23	1	A:54-56	3
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	0	-	-

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:56
 aligned with CBX7_HUMAN | O95931 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:56
                                    16        26        36        46        56      
            CBX7_HUMAN    7 GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE 62
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains 2l1bA00 A:1-56  [code=2.40.50.40, no name defined]       CATH domains
               Pfam domains ----Chromo-2l1bA01 A:5-54                             -- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee..eeeeeeee........eeee.hhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----CHROMO_2  PDB: A:5-56 UniProt: 11-69                 PROSITE (1)
                PROSITE (2) ---------------------CHROMO_1  PDB: A:22-4-------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1b        Exon 1.2a      ---------------------1.4 Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3a  PDB: A:32-54-- Transcript 1 (2)
                  2l1b A  1 GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE 56
                                    10        20        30        40        50

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:15
                                    29     
          Q92133_XENLA   20 QLATKAARKSAPATG 34
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ....eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  2l1b B 19 QLATKAARkSAPATG 33
                                    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 '\|'

(no "SCOP Domain" information available for 2L1B)

NMR Structure

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)

2l1bA00

A:1-56

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Tudor (88)

Family: Chromo (16)

Homo sapiens (Human) (8)

Chromo-2l1bA01

A:5-54

NMR Structure(hide GO term definitions)

Chain A (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.

Chain B (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.

NMR Structure
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	CBX7_HUMAN \| O95931	:	2k1b 2l12 3gs2 4mn3 5epj
	Q92133_XENLA \| Q92133	:	2hue 3gv6
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Description

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Ligands, Modified Residues, Ions (1, 1)

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Exons (4, 4)

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Gene Ontology (20, 21)

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