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Yorodumi- PDB-6hms: Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hms | ||||||
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Title | Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA | ||||||
Components |
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Keywords | REPLICATION / DNA / polymerase D / Pyrococcus | ||||||
Function / homology | Function and homology information exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / DNA catabolic process / DNA strand elongation involved in DNA replication / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å | ||||||
Authors | Raia, P. / Carroni, M. / Sauguet, L. | ||||||
Funding support | France, 1items
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Citation | Journal: PLoS Biol / Year: 2019 Title: Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. Authors: Pierre Raia / Marta Carroni / Etienne Henry / Gérard Pehau-Arnaudet / Sébastien Brûlé / Pierre Béguin / Ghislaine Henneke / Erik Lindahl / Marc Delarue / Ludovic Sauguet / Abstract: PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal ...PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome. | ||||||
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 | 6hms.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hms.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hms_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6hms_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6hms_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 6hms_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/6hms ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hms | HTTPS FTP |
-Related structure data
Related structure data | 0244MC 6hmfC 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
-DNA polymerase II ... , 2 types, 2 molecules AB
#1: Protein | Mass: 45078.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: polB, PYRAB01210, PAB2266 / Production host: Escherichia coli (E. coli) References: UniProt: Q9V2F3, DNA-directed DNA polymerase, exodeoxyribonuclease I |
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#2: Protein | Mass: 144418.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: polC, PYRAB01200, PAB2404 / Production host: Escherichia coli (E. coli) References: UniProt: Q9V2F4, DNA-directed DNA polymerase, exodeoxyribonuclease I |
-DNA chain , 2 types, 2 molecules PT
#3: DNA chain | Mass: 4635.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi (archaea) |
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#4: DNA chain | Mass: 4851.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi (archaea) |
-Non-polymers , 2 types, 5 molecules
#5: Chemical | ChemComp-FE / |
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#6: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
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: 1 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8774 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 7.1 Å | ||||||||||||||||||||||||
Refine LS restraints |
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