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Yorodumi- PDB-8hoy: Cryo-EM structure of monkeypox virus DNA replication holoenzyme F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hoy | ||||||
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Title | Cryo-EM structure of monkeypox virus DNA replication holoenzyme F8, A22 and E4 complex without DNA at 2.76 angostram | ||||||
Components |
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Keywords | VIRAL PROTEIN / DNA replication machinery / DNA polymerase / B-family DNA polymerase / uracil-DNA glycosylase / MPXV / orthopoxvirus / poxviridae / DNA processivity factor | ||||||
Function / homology | Function and homology information nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / viral DNA genome replication / uracil DNA N-glycosylase activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA replication / DNA-directed DNA polymerase ...nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / viral DNA genome replication / uracil DNA N-glycosylase activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Monkeypox virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | ||||||
Authors | Xu, Y. / Wu, Y. / Zhang, Y. / Fan, R. / Yang, Y. / Li, D. / Yang, B. / Zhang, Z. / Dong, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res / Year: 2023 Title: Cryo-EM structures of human monkeypox viral replication complexes with and without DNA duplex. Authors: Yunxia Xu / Yaqi Wu / Yuanyuan Zhang / Ruixin Fan / Yaxue Yang / Danyang Li / Shimin Zhu / Biao Yang / Zhengyu Zhang / Changjiang Dong / | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hoy.cif.gz | 343.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hoy.ent.gz | 270.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hoy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hoy_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8hoy_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8hoy_validation.xml.gz | 55.7 KB | Display | |
Data in CIF | 8hoy_validation.cif.gz | 81 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/8hoy ftp://data.pdbj.org/pub/pdb/validation_reports/ho/8hoy | HTTPS FTP |
-Related structure data
Related structure data | 34927MC 8hdzC 8hpaC C: citing same article (ref.) M: map data used to model this data |
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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
#1: Protein | Mass: 120041.156 Da / Num. of mol.: 1 / Mutation: L108F, W411L Source method: isolated from a genetically manipulated source Details: MPXV DNA replication machinery catalytic subunit F8 Source: (gene. exp.) Monkeypox virus / Gene: F8L Production host: Insect expression vector pBlueBacmsGCA1His (others) References: UniProt: Q5IXW8 |
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#2: Protein | Mass: 49203.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: A22R Production host: Insect expression vector pBlueBachsGCA1 (others) References: UniProt: Q5IXP2 |
#3: Protein | Mass: 27883.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: E4R Production host: Insect expression vector pBlueBachsGCA1 (others) References: UniProt: Q5IXS4, uracil-DNA glycosylase |
-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: Monkeypox virus replication holoenzyme F8-A22-E4 complex without DNA Type: COMPLEX / Details: F8-A22-E4 complex / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 191 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Monkeypox virus |
Source (recombinant) | Organism: Baculovirus expression vector pFastBac1-HM |
Buffer solution | pH: 8 Details: 25mM HEPES pH 8.0, 300mM NaCl, 5% (w/v) glycerol, and 1 mM TCEP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This is a complex of F8-A22-E4 |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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Image processing | Details: The selected movies are corrected with motion correct | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Details: 11,662,000 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 343570 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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