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

Asym./Biol. Unit (Jmol Viewer)

Title :   COMPLEX OF THE S. CEREVISIAE ORC1 AND SIR1 INTERACTING DOMAINS

Authors :   Z. Hou, D. A. Bernstein, C. A. Fox, J. L. Keck

Date :   25 Apr 05 (Deposition) - 07 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Protein Complex, Bah Domain, Oir Domain, Transcription-Replication Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Hou, D. A. Bernstein, C. A. Fox, J. L. Keck
Structural Basis Of The Sir1-Origin Recognition Complex Interaction In Transcriptional Silencing.
Proc. Natl. Acad. Sci. Usa V. 102 8489 2005
PubMed-ID: 15932939 | Reference-DOI: 10.1073/PNAS.0503525102

Molecule 1 - ORIGIN RECOGNITION COMPLEX SUBUNIT 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	BAH DOMAIN OF ORC1
	Gene	:	ORC1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	ORIGIN RECOGNITION COMPLEX PROTEIN 120 KDA SUBUNIT

Molecule 2 - REGULATORY PROTEIN SIR1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	OIR* DOMAIN OF SIR1
	Gene	:	SIR1
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	SILENT INFORMATION REGULATOR 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ZHI)

(no "Site" information available for 1ZHI)

(no "SS Bond" information available for 1ZHI)

(no "Cis Peptide Bond" information available for 1ZHI)

(no "SAP(SNP)/Variant" information available for 1ZHI)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BAH	PS51038	BAH domain profile.	ORC1_YEAST	48-188	1	A:48-188

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YKR101W	1	YKR101W.1	XI:640178-642142	1965	SIR1_YEAST	1-654	654	1	B:487-611	125

2.1	YML065W	1	YML065W.1	XIII:142210-144954	2745	ORC1_YEAST	1-914	914	1	A:10-214 (gaps)	205

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
	(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:195
 aligned with ORC1_YEAST | P54784 from UniProtKB/Swiss-Prot  Length:914

    Alignment length:205
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
           ORC1_YEAST    10 GWEIITTDEQGNIIDGGQKRLRRRGAKTEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIKKVEPREAQEYLKDLTLP 214
               SCOP domains d1zhia_ A: Origin          -recognition complex protein 120kDa subunit, Orc1p                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------BAH-1zhiA01 A:48-188                                                                                                                         -------------------------- Pfam domains
         Sec.struct. author .eeeeee..........----------.eeeeee.....ee....eeeeee....eeeeeeeeeeee......eeeeeeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...eeeeeeeeeeehhh.eeeeeeeeehhhhhhhhhhh....eeeeeee........ee.hhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------BAH  PDB: A:48-188 UniProt: 48-188                                                                                                           -------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:10-214 (gaps) UniProt: 1-914 [INCOMPLETE]                                                                                                                                                    Transcript 2
                 1zhi A  10 GWEIITTDEQGNIIDGG----------TEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIKKVEPREAQEYLKDLTLP 214
                                    19      |  -       |39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
                                           26         37

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with SIR1_YEAST | P21691 from UniProtKB/Swiss-Prot  Length:654

    Alignment length:125
                                   472       482       492       502       512       522       532       542       552       562       572       582     
           SIR1_YEAST   463 EEYVSPRFLVADGFLIDLAEEKPINPKDPRLLTLLKDHQRAMIDQMNLVKWNDFKKYQDPIPLKAKTLFKFCKQIKKKFLRGADFKLHTLPTEANLKYEPERMTVLCSCVPILLDDQTVQYLYDD 587
               SCOP domains d1zhib1 B:487-611 Regulatory protein SIR1                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Sir1-1zhiB01 B:487-611                                                                                                        Pfam domains
         Sec.struct. author .ee....eeee..eeee....eee.....hhhhhhhhhhhhhhhh....hhhhhh.....ee..hhhhhhhh..eeeeeee.....ee..............eeeeeeeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:487-611 UniProt: 1-654 [INCOMPLETE]                                                                          Transcript 1
                 1zhi B 487 EEYVSPRFLVADGFLIDLAEEKPINPKDPRLLTLLKDHQRAMIDQMNLVKWNDFKKYQDPIPLKAKTLFKFCKQIKKKFLRGADFKLHTLPTEANLKYEPERMTVLASCVPILLDDQTVQYLYDD 611
                                   496       506       516       526       536       546       556       566       576       586       596       606

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 "CATH Domain" information available for 1ZHI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ORC1_YEAST | P54784)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	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: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).
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006270	DNA replication initiation	The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
	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:0006267	pre-replicative complex assembly involved in nuclear cell cycle DNA replication	The aggregation, arrangement and bonding together of a set of components to form the nuclear pre-replicative complex, a protein-DNA complex that forms at the eukaryotic DNA replication origin and is required for replication initiation.
cellular component
	GO:0031261	DNA replication preinitiation complex	A protein-DNA complex assembled at eukaryotic DNA replication origins immediately prior to the initiation of DNA replication. The preinitiation complex is formed by the assembly of additional proteins onto an existing prereplicative complex. In budding yeast, the additional proteins include Cdc45p, Sld2p, Sld3p, Dpb11p, DNA polymerases, and others; in fission yeast the GINS complex is present.
	GO:0005664	nuclear origin of replication recognition complex	A multisubunit complex that is located at the replication origins of a chromosome in the nucleus.
	GO:0005656	nuclear pre-replicative complex	A protein-DNA complex assembled at eukaryotic DNA replication origins during late mitosis and G1, allowing the origin to become competent, or 'licensed', for replication. The complex normally includes the origin recognition complex (ORC), Cdc6, Cdt1 and the MiniChromosome Maintenance (Mcm2-7) proteins.
	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 (SIR1_YEAST | P21691)

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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
	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:0006343	establishment of chromatin silencing	The initial formation of a transcriptionally silent chromatin structure such as heterochromatin.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005677	chromatin silencing complex	Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	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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	1zhi
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	SIR1_YEAST \| P21691
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UniProtKB/Swiss-Prot
	ORC1_YEAST \| P54784	:	1m4z 1zbx 5udb 5v8f
	SIR1_YEAST \| P21691	:	1z1a 1zbx

1m4z	BAH DOMAIN OF ORC1P
1z1a	ORC1-INTERACTING DOMAIN OF SIR1

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