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Yorodumi- PDB-6wjv: Structure of the Saccharomyces cerevisiae polymerase epsilon holo... -
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-Basic information
Entry | Database: PDB / ID: 6wjv | ||||||||||||
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Title | Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme | ||||||||||||
Components |
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Keywords | CELL CYCLE / DNA replication / DNA polymerase | ||||||||||||
Function / homology | Function and homology information : / : / chromatin remodeling => GO:0006338 / : / CHRAC / DNA-templated DNA replication maintenance of fidelity / gene conversion / DNA replication initiation / epsilon DNA polymerase complex / SUMO binding ...: / : / chromatin remodeling => GO:0006338 / : / CHRAC / DNA-templated DNA replication maintenance of fidelity / gene conversion / DNA replication initiation / epsilon DNA polymerase complex / SUMO binding / Activation of the pre-replicative complex / nucleotide-excision repair, DNA gap filling / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mitotic sister chromatid cohesion / leading strand elongation / nuclear replication fork / Dual incision in TC-NER / error-prone translesion synthesis / nucleosomal DNA binding / base-excision repair, gap-filling / replication fork / base-excision repair / heterochromatin formation / chromatin DNA binding / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / mitotic cell cycle / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / protein heterodimerization activity / nucleotide binding / mRNA binding / DNA damage response / DNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Yuan, Z. / Georgescu, R. / Schauer, G.D. / O'Donnell, M. / Li, H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure of the polymerase ε holoenzyme and atomic model of the leading strand replisome. Authors: Zuanning Yuan / Roxana Georgescu / Grant D Schauer / Michael E O'Donnell / Huilin Li / Abstract: The eukaryotic leading strand DNA polymerase (Pol) ε contains 4 subunits, Pol2, Dpb2, Dpb3 and Dpb4. Pol2 is a fusion of two B-family Pols; the N-terminal Pol module is catalytic and the C-terminal ...The eukaryotic leading strand DNA polymerase (Pol) ε contains 4 subunits, Pol2, Dpb2, Dpb3 and Dpb4. Pol2 is a fusion of two B-family Pols; the N-terminal Pol module is catalytic and the C-terminal Pol module is non-catalytic. Despite extensive efforts, there is no atomic structure for Pol ε holoenzyme, critical to understanding how DNA synthesis is coordinated with unwinding and the DNA path through the CMG helicase-Pol ε-PCNA clamp. We show here a 3.5-Å cryo-EM structure of yeast Pol ε revealing that the Dpb3-Dpb4 subunits bridge the two DNA Pol modules of Pol2, holding them rigid. This information enabled an atomic model of the leading strand replisome. Interestingly, the model suggests that an OB fold in Dbp2 directs leading ssDNA from CMG to the Pol ε active site. These results complete the DNA path from entry of parental DNA into CMG to exit of daughter DNA from PCNA. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6wjv.cif.gz | 459.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wjv.ent.gz | 366.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wjv_validation.pdf.gz | 759 KB | Display | wwPDB validaton report |
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Full document | 6wjv_full_validation.pdf.gz | 780.8 KB | Display | |
Data in XML | 6wjv_validation.xml.gz | 68.1 KB | Display | |
Data in CIF | 6wjv_validation.cif.gz | 103.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/6wjv ftp://data.pdbj.org/pub/pdb/validation_reports/wj/6wjv | HTTPS FTP |
-Related structure data
Related structure data | 21701MC 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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1 |
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-Components
#1: Protein | Mass: 255992.484 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: POL2, DUN2, YNL262W, N0825 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21951, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters |
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#2: Protein | Mass: 78425.852 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: DPB2, YPR175W, P9705.7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P24482 |
#3: Protein | Mass: 22694.014 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: DPB3, YBR278W, YBR2015 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27344 |
#4: Protein | Mass: 22029.484 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: DPB4, YDR121W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04603 |
#5: Chemical | ChemComp-ZN / |
Has ligand of interest | Y |
-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: DNA polymerase epsilon / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Plasmid: pRS |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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 |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187298 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |