2RSN - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE CHROMODOMAIN OF CHP1 IN COMPLEX WITH H3K9ME3 PEPTIDE

Authors :   H. Shimojo, Y. Nishimura

Date :   18 Apr 12 (Deposition) - 29 Aug 12 (Release) - 29 Aug 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Chromodomain, Protein-Peptide Complex, Rna-Mediated Gene Silencing, Chromosomal Protein, Methylation, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ishida, H. Shimojo, A. Hayashi, R. Kawaguchi, Y. Ohtani, K. Uegaki, Y. Nishimura, J. Nakayama
Intrinsic Nucleic Acid-Binding Activity Of Chp1 Chromodomai Is Required For Heterochromatic Gene Silencing
Mol. Cell V. 47 228 2012
PubMed-ID: 22727667 | Reference-DOI: 10.1016/J.MOLCEL.2012.05.017

Molecule 1 - CHROMO DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PCOLD
	Expression System Vector Type	:	VECTOR
	Fragment	:	CHROMO DOMAIN
	Gene	:	CHP1
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	284812
	Strain	:	972

Molecule 2 - PEPTIDE FROM HISTONE H3
	Chains	:	B
	Engineered	:	YES
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Other Details	:	SYNTHETIC 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 2RSN)

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

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

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

NMR Structure (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_1	PS00322	Histone H3 signature 1.	H3_YEAST	15-21	1	B:14-17
2	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CHP1_SCHPO	22-74	1	A:22-74
3	CHROMO_1	PS00598	Chromo domain signature.	CHP1_SCHPO	40-60	1	A:40-60

NMR Structure * (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_1	PS00322	Histone H3 signature 1.	H3_YEAST	15-21	1	B:14-17
2	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CHP1_SCHPO	22-74	1	A:22-74
3	CHROMO_1	PS00598	Chromo domain signature.	CHP1_SCHPO	40-60	1	A:40-60

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL031C	1	YNL031C.1	XIV:576052-575642	411	H3_YEAST	1-136	136	1	B:1-18 (gaps)	41

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:75
 aligned with CHP1_SCHPO | Q10103 from UniProtKB/Swiss-Prot  Length:960

    Alignment length:75
                                    10        20        30        40        50        60        70     
            CHP1_SCHPO    1 MVSVKPLPDIDSNEGETDADVYEVEDILADRVNKNGINEYYIKWAGYDWYDNTWEPEQNLFGAEKVLKKWKKRKK 75
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhheeeeeeeeeee.....eeeeeeee..hhhhheeee.hhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------CHROMO_2  PDB: A:22-74 UniProt: 22-74                - PROSITE (1)
                PROSITE (2) ---------------------------------------CHROMO_1  PDB: A:40-6--------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------- Transcript
                  2rsn A  1 MVSVKPLPDIDSNEGETDADVYEVEDILADRVNKNGINEYYIKWAGYDWYDNTWEPEQNLFGAEKVLKKWKKRKK 75
                                    10        20        30        40        50        60        70

Chain B from PDB  Type:PROTEIN  Length:18
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:41
                                    11        21        31        41 
              H3_YEAST    2 ARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRY 42
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ....eee..........-----------------------. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE -------------HISTONE--------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-18 (gaps) [INCOMPLETE] Transcript 1
                  2rsn B  1 ARTKQTARkSTGGKAPR-----------------------Y 18
                                    10      |  -         -         -|
                                    9-M3L  17                      18

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 2RSN)

(no "CATH Domain" information available for 2RSN)

(no "Pfam Domain" information available for 2RSN)

NMR Structure(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 B (H3_YEAST | P61830)

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:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0009303	rRNA transcription	The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
	GO:0043935	sexual sporulation resulting in formation of a cellular spore	The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
	GO:0043505	CENP-A containing nucleosome	A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3).
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	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: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.
	GO:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

NMR Structure
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

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