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Yorodumi- PDB-8wpf: Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wpf | ||||||
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Title | Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with exogenous DNA bearing one abasic site | ||||||
Components |
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Keywords | VIRAL PROTEIN / Viral DNA replication / monkeypox virus / polymerase / H5 | ||||||
Function / homology | 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Monkeypox virus synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Wang, X. / Li, N. / Gao, N. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5. Authors: Xiaohan Wang / Liangwen Ma / Ningning Li / Ning Gao / Abstract: The DNA replication of mpox virus is performed by the viral polymerase F8 and also requires other viral factors, including processivity factor A22, uracil DNA glycosylase E4, and phosphoprotein H5. ...The DNA replication of mpox virus is performed by the viral polymerase F8 and also requires other viral factors, including processivity factor A22, uracil DNA glycosylase E4, and phosphoprotein H5. However, the molecular roles of these viral factors remain unclear. Here, we characterize the structures of F8-A22-E4 and F8-A22-E4-H5 complexes in the presence of different primer-template DNA substrates. E4 is located upstream of F8 on the template single-stranded DNA (ssDNA) and is catalytically active, highlighting a functional coupling between DNA base-excision repair and DNA synthesis. Moreover, H5, in the form of tetramer, binds to the double-stranded DNA (dsDNA) region downstream of F8 in a similar position as PCNA (proliferating cell nuclear antigen) does in eukaryotic polymerase complexes. Omission of H5 or disruption of its DNA interaction showed a reduced synthesis of full-length DNA products. These structures provide snapshots for the working cycle of the polymerase and generate insights into the mechanisms of these essential factors in viral DNA replication. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wpf.cif.gz | 392.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wpf.ent.gz | 306.1 KB | Display | PDB format |
PDBx/mmJSON format | 8wpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wpf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8wpf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8wpf_validation.xml.gz | 63 KB | Display | |
Data in CIF | 8wpf_validation.cif.gz | 92.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/8wpf ftp://data.pdbj.org/pub/pdb/validation_reports/wp/8wpf | HTTPS FTP |
-Related structure data
Related structure data | 37715MC 8wpeC 8wpkC 8wppC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 7 molecules ABCDEFG
#1: Protein | Mass: 117147.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GenBank: URK20494.1 / Source: (gene. exp.) Monkeypox virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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#2: Protein | Mass: 50466.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GenBank: URK20570.1 / Source: (gene. exp.) Monkeypox virus / Gene: A22R / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
#3: Protein | Mass: 25107.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GenBank: URK20538.1 / Source: (gene. exp.) Monkeypox virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
#4: Protein | Mass: 23107.074 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: GenBank: URK20532.1 / Source: (gene. exp.) Monkeypox virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
-DNA chain , 2 types, 2 molecules HI
#5: DNA chain | Mass: 10802.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 14643.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 2 molecules
#7: Chemical | ChemComp-D3T / |
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#8: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | Y |
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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 |
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Source (natural) | Organism: Monkeypox virus | ||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||
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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 782000 / Symmetry type: POINT |