+Open data
-Basic information
Entry | Database: PDB / ID: 6v8p | ||||||
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Title | Structure of DNA Polymerase Zeta (Apo) | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA REPLICATION / DNA REPAIR / TRANSLESION DNA SYNTHESIS / DNA POLYMERASE | ||||||
Function / homology | Function and homology information delta DNA polymerase complex / DNA amplification / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer ...delta DNA polymerase complex / DNA amplification / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / double-strand break repair via break-induced replication / lagging strand elongation / postreplication repair / DNA strand elongation involved in DNA replication / DNA metabolic process / error-free translesion synthesis / leading strand elongation / mismatch repair / error-prone translesion synthesis / nucleotide-excision repair / double-strand break repair via homologous recombination / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin / mitochondrion / DNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Malik, R. / Gomez-Llorente, Y. / Ubarretxena-Belandia, I. / Aggarwal, A.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Structure and mechanism of B-family DNA polymerase ζ specialized for translesion DNA synthesis. Authors: Radhika Malik / Mykhailo Kopylov / Yacob Gomez-Llorente / Rinku Jain / Robert E Johnson / Louise Prakash / Satya Prakash / Iban Ubarretxena-Belandia / Aneel K Aggarwal / Abstract: DNA polymerase ζ (Polζ) belongs to the same B-family as high-fidelity replicative polymerases, yet is specialized for the extension reaction in translesion DNA synthesis (TLS). Despite its ...DNA polymerase ζ (Polζ) belongs to the same B-family as high-fidelity replicative polymerases, yet is specialized for the extension reaction in translesion DNA synthesis (TLS). Despite its importance in TLS, the structure of Polζ is unknown. We present cryo-EM structures of the Saccharomyces cerevisiae Polζ holoenzyme in the act of DNA synthesis (3.1 Å) and without DNA (4.1 Å). Polζ displays a pentameric ring-like architecture, with catalytic Rev3, accessory Pol31' Pol32 and two Rev7 subunits forming an uninterrupted daisy chain of protein-protein interactions. We also uncover the features that impose high fidelity during the nucleotide-incorporation step and those that accommodate mismatches and lesions during the extension reaction. Collectively, we decrypt the molecular underpinnings of Polζ's role in TLS and provide a framework for new cancer therapeutics. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6v8p.cif.gz | 381 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v8p.ent.gz | 277.9 KB | Display | PDB format |
PDBx/mmJSON format | 6v8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v8p ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v8p | HTTPS FTP |
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-Related structure data
Related structure data | 21108MC 6v93C 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: 177068.516 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: REV3, PSO1, YPL167C, P2535 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14284, DNA-directed DNA polymerase | ||||||||
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#2: Protein | Mass: 28791.654 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: REV7, YIL139C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38927 #3: Protein | | Mass: 55987.352 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: POL31, HUS2, HYS2, SDP5, YJR006W, J1427, YJR83.7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P46957, DNA-directed DNA polymerase #4: Protein | | Mass: 40377.715 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: POL32, YJR043C, J1626 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47110 #5: Chemical | ChemComp-SF4 / | 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: Apo / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER |
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: vitreous ice |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 87.62 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 9758 |
-Processing
Software | Name: PHENIX / Version: dev_3488: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 311800 / Symmetry type: POINT | ||||||||||||||||||||||||
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