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- PDB-8hdz: Monkeypox virus DNA replication holoenzyme F8, A22 and E4 complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hdz | ||||||
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Title | Monkeypox virus DNA replication holoenzyme F8, A22 and E4 complex in an apo form | ||||||
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![]() | VIRAL PROTEIN / DNA replication machinery / F8 / A22 / E4 / DNA polymerase / B-family DNA polymerase / uracil-DNA glycosylase / MPXV / orthopoxvirus / poxviridae / DNA processivity factor | ||||||
Function / homology | ![]() viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA replication / DNA-directed DNA polymerase ...viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease 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 | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å | ||||||
![]() | Xu, Y. / Wu, Y. / Zhang, Y. / Fan, R. / Yang, Y. / Li, D. / Yang, B. / Zhang, Z. / Dong, C. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 306.5 KB | Display | ![]() |
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PDB format | ![]() | 241.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 51.2 KB | Display | |
Data in CIF | ![]() | 73.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34684MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 120041.156 Da / Num. of mol.: 1 / Mutation: L108F, M411L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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.) ![]() ![]() |
#3: Protein | Mass: 27883.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Monkeypox virus replication holoenzyme F8-A22-E4 complex Type: COMPLEX / Details: F8-A22-E4 complex / Entity ID: #1, #3, #2 / Source: RECOMBINANT |
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Molecular weight | Value: 191 kDa/nm / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
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 mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
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) |
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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: 19,555,002 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 632071 / Num. of class averages: 4 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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