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Yorodumi- PDB-5zr1: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72... -
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-Basic information
Entry | Database: PDB / ID: 5zr1 | ||||||
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Title | Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Origin Recognition Complex / DNA replication initiation / 72-bp origin DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information CDC6 association with the ORC:origin complex / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nucleosome organization / nuclear pre-replicative complex / Activation of ATR in response to replication stress ...CDC6 association with the ORC:origin complex / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nucleosome organization / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / Orc1 removal from chromatin / regulation of DNA replication / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / nucleosome binding / chromosome, telomeric region / chromatin binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Li, N. / Lam, W.H. / Zhai, Y. / Cheng, J. / Cheng, E. / Zhao, Y. / Gao, N. / Tye, B.K. | ||||||
Citation | Journal: Nature / Year: 2018 Title: Structure of the origin recognition complex bound to DNA replication origin. Authors: Ningning Li / Wai Hei Lam / Yuanliang Zhai / Jiaxuan Cheng / Erchao Cheng / Yongqian Zhao / Ning Gao / Bik-Kwoon Tye / Abstract: The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the ...The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the Saccharomyces cerevisiae ORC bound to a 72-base-pair origin DNA sequence that contains the ARS consensus sequence (ACS) and the B1 element. The ORC encircles DNA through extensive interactions with both phosphate backbone and bases, and bends DNA at the ACS and B1 sites. Specific recognition of thymine residues in the ACS is carried out by a conserved basic amino acid motif of Orc1 in the minor groove, and by a species-specific helical insertion motif of Orc4 in the major groove. Moreover, similar insertions into major and minor grooves are also embedded in the B1 site by basic patch motifs from Orc2 and Orc5, respectively, to contact bases and to bend DNA. This work pinpoints a conserved role of ORC in modulating DNA structure to facilitate origin selection and helicase loading in eukaryotes. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 5zr1.cif.gz | 525.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zr1.ent.gz | 406.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zr1_validation.pdf.gz | 988.4 KB | Display | wwPDB validaton report |
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Full document | 5zr1_full_validation.pdf.gz | 1005.2 KB | Display | |
Data in XML | 5zr1_validation.xml.gz | 67 KB | Display | |
Data in CIF | 5zr1_validation.cif.gz | 103.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/5zr1 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/5zr1 | HTTPS FTP |
-Related structure data
Related structure data | 6941MC 6942C 6943C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Origin recognition complex subunit ... , 6 types, 6 molecules ABCDEF
#1: Protein | Mass: 104546.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ORC1, YML065W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P54784 |
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#2: Protein | Mass: 71342.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ORC2, RRR1, SIR5, YBR060C, YBR0523 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32833 |
#3: Protein | Mass: 72161.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ORC3, OAF1, OIF1, YLL004W, L1365 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P54790 |
#4: Protein | Mass: 60772.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ORC4, YPR162C, P9325.5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P54791 |
#5: Protein | Mass: 55347.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ORC5, YNL261W, N0834 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P50874 |
#6: Protein | Mass: 50369.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ORC6, AAP1, YHR118C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38826 |
-72bp-oring DNA, ACS305, ... , 2 types, 2 molecules GH
#7: DNA chain | Mass: 22203.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
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#8: DNA chain | Mass: 22174.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
-Non-polymers , 2 types, 6 molecules
#9: Chemical | #10: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element Type: COMPLEX Details: Saccharomyces Cerevisiae Origin Recognition Complex (Orc1-6, chain A-F) Bound to a 72-bp Origin DNA (a 72-bp dsDNA chain G-H) containing ACS and B1 element Entity ID: #1-#8 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 52.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164857 / Symmetry type: POINT | ||||||||||||||||||||||||
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