3G7L - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CHROMODOMAIN OF CHP1 IN COMPLEX WITH HISTONE H3K9ME3 PEPTIDE

Authors :   T. Schalch, L. Joshua-Tor

Date :   10 Feb 09 (Deposition) - 21 Apr 09 (Release) - 21 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,P

Keywords :   Chromodomain, Protein-Peptide Complex, Silencing, Cell Cycle, Chromosome Partition, Dna-Binding, Nucleus, Rna- Mediated Gene Silencing, Acetylation, Chromosomal Protein, Dna Damage, Dna Repair, Methylation, Nucleosome Core, Phosphoprotein, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Schalch, G. Job, V. J. Noffsinger, S. Shanker, C. Kuscu, L. Joshua-Tor, J. F. Partridge
High-Affinity Binding Of Chp1 Chromodomain To K9 Methylated Histone H3 Is Required To Establish Centromeric Heterochromatin
Mol. Cell V. 34 36 2009
PubMed-ID: 19362535 | Reference-DOI: 10.1016/J.MOLCEL.2009.02.024
(for further references see the PDB file header)

Molecule 1 - CHROMO DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A-SUMO
	Expression System Strain	:	BL21 (DE3) RIPL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CHROMODOMAIN (UNP RESIDUES 15 TO 75)
	Gene	:	CHP1, SPAC18G6.02C
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896

Molecule 2 - HISTONE H3.1/H3.2
	Chains	:	P
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 2 TO 17
	Mutation	:	YES
	Other Details	:	PEPTIDE SYNTHESIS BY PROTEIN PEPTIDE RESEARCH LDT., HAMPSHIRE UK.
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ZN A:2 , TYR A:47 , ASP A:48 , TYR A:50 , ASP A:51 , ZN A:76	BINDING SITE FOR RESIDUE ACY A 1
2	AC2	SOFTWARE	ACY A:1 , ZN A:2 , ASP A:48 , ASP A:51	BINDING SITE FOR RESIDUE ZN A 76
3	AC3	SOFTWARE	ACY A:1 , ASP A:51 , ZN A:76	BINDING SITE FOR RESIDUE ZN A 2
4	AC4	SOFTWARE	ASP A:30 , TRP A:70	BINDING SITE FOR RESIDUE ZN A 3
5	AC5	SOFTWARE	ASP A:26 , HOH A:93	BINDING SITE FOR RESIDUE ZN A 4

(no "SS Bond" information available for 3G7L)

(no "Cis Peptide Bond" information available for 3G7L)

(no "SAP(SNP)/Variant" information available for 3G7L)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CHP1_SCHPO	22-74	1	A:22-73
2	CHROMO_1	PS00598	Chromo domain signature.	CHP1_SCHPO	40-60	1	A:40-60

(no "Exon" information available for 3G7L)

Asymmetric/Biological 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:55
 aligned with CHP1_SCHPO | Q10103 from UniProtKB/Swiss-Prot  Length:960

    Alignment length:55
                                    28        38        48        58        68     
            CHP1_SCHPO   19 ADVYEVEDILADRVNKNGINEYYIKWAGYDWYDNTWEPEQNLFGAEKVLKKWKKR 73
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains 3g7lA00 A:19-73  [code=2.40.50.40, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeee...hhhhheeee.hhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CHROMO_2  PDB: A:22-73 UniProt: 22-74                PROSITE (1)
                PROSITE (2) ---------------------CHROMO_1  PDB: A:40-6------------- PROSITE (2)
                 Transcript ------------------------------------------------------- Transcript
                  3g7l A 19 ADVYEVEDILADRVNKNGINEYYIKWAGYDWYDNTWEPEQNLFGAEKVLKKWKKR 73
                                    28        38        48        58        68

Chain P from PDB  Type:PROTEIN  Length:7
 aligned with H31_SCHPO | P09988 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:7
             H31_SCHPO    5 KQTARKS 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
                  3g7l P  4 KQTARkS 10
                                 | 
                                 9-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 3G7L)

Asymmetric/Biological 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)

Fission yeast (Schizosaccharomyces pombe) (2)

3g7lA00

A:19-73

(no "Pfam Domain" information available for 3G7L)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CHP1_SCHPO | Q10103)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0031493	nucleosomal histone binding	Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0034613	cellular protein localization	Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
	GO:1990141	chromatin silencing at centromere outer repeat region	Repression of transcription of DNA at the outer repeat region of a regional centromere by altering the structure of chromatin.
	GO:0030466	chromatin silencing at silent mating-type cassette	Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
	GO:0006348	chromatin silencing at telomere	Repression of transcription of telomeric DNA by altering the structure of chromatin.
	GO:0031048	chromatin silencing by small RNA	Repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.
	GO:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	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:0031508	pericentric heterochromatin assembly	The assembly of chromatin into heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
	GO:0071459	protein localization to chromosome, centromeric region	Any process in which a protein is transported to, or maintained at, the centromeric region of a chromosome.
cellular component
	GO:0030958	RITS complex	A protein complex required for heterochromatin assembly; contains an Argonaute homolog, a chromodomain protein, and at least one additional protein; named for RNA-induced initiation of transcriptional gene silencing.
	GO:0034507	chromosome, centromeric outer repeat region	The portion of the centromeric region of a chromosome that flanks the core region, encompassing repeated regions of a chromosome centromere and the proteins that bind to it.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0031934	mating-type region heterochromatin	Heterochromatic regions of the chromosome found at silenced mating-type loci.
	GO:0044732	mitotic spindle pole body	The microtubule organizing center that forms as part of the mitotic cell cycle; functionally homologous to the animal cell centrosome.
	GO:0031618	nuclear pericentric heterochromatin	Nuclear heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
	GO:1990707	nuclear subtelomeric heterochromatin	Heterochromatic regions of the chromosome found at the subtelomeric regions of a chromosome in the nucleus.
	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:0005816	spindle pole body	The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.

Chain P (H31_SCHPO | P09988)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006974	cellular response to DNA damage stimulus	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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
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:0031934	mating-type region heterochromatin	Heterochromatic regions of the chromosome found at silenced mating-type loci.
	GO:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	GO:0031618	nuclear pericentric heterochromatin	Nuclear heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
	GO:1990707	nuclear subtelomeric heterochromatin	Heterochromatic regions of the chromosome found at the subtelomeric regions of a chromosome in the nucleus.
	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/Biological Unit
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	CHP1_SCHPO \| Q10103	:	2rsn 3tix
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (5, 5)

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