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- PDB-9nsp: MPXV replisome bound to ssDNA -

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Basic information

Entry
Database: PDB / ID: 9nsp
TitleMPXV replisome bound to ssDNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA polymerase
  • DNA polymerase processivity factor component OPG148
  • Uncoating factor OPG117
  • Uracil-DNA glycosylase
KeywordsVIRAL PROTEIN/DNA / MPXV / replisome / replication / VIRAL PROTEIN / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / viral DNA genome replication / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / DNA-directed DNA polymerase / host cell cytoplasm / DNA-directed DNA polymerase activity / DNA replication ...uracil-DNA glycosylase / uracil DNA N-glycosylase activity / viral DNA genome replication / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / DNA-directed DNA polymerase / host cell cytoplasm / DNA-directed DNA polymerase activity / DNA replication / hydrolase activity / nucleotide binding / DNA repair / DNA binding / ATP binding
Similarity search - Function
DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / Chordopoxvirus A20R / Chordopoxvirus A20R protein / DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / : / Bacteriophage/plasmid primase, P4, C-terminal ...DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / Chordopoxvirus A20R / Chordopoxvirus A20R protein / DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / : / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / : / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase / Uncoating factor OPG117 / DNA polymerase processivity factor component OPG148 / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMonkeypox virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsYu, Z. / Abraham, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2026
Title: Structure and operating principles of a monkeypox virus replisome
Authors: Yu, Z. / Sathyanarayana, P. / Tan, J.M.J.T. / Hu, S. / Fan, X. / Gao, A. / Kranzusch, P.J. / Loparo, J.J. / Abraham, J.
History
DepositionMar 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Uncoating factor OPG117
E: Uncoating factor OPG117
A: DNA polymerase
C: DNA polymerase processivity factor component OPG148
B: Uracil-DNA glycosylase
T: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
I: Uncoating factor OPG117
H: Uncoating factor OPG117
J: Uncoating factor OPG117
K: Uncoating factor OPG117
hetero molecules


Theoretical massNumber of molelcules
Total (without water)743,12511
Polymers743,05910
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 9 molecules DEIHJKACB

#1: Protein
Uncoating factor OPG117


Mass: 90476.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG117, MPXVgp100 / Production host: Homo sapiens (human)
References: UniProt: A0A7H0DN89, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein DNA polymerase


Mass: 117113.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG071, POL, MPXVgp056 / Production host: Homo sapiens (human)
References: UniProt: A0A7H0DN44, DNA-directed DNA polymerase
#3: Protein DNA polymerase processivity factor component OPG148


Mass: 49203.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG148, MPXVgp132 / Production host: Homo sapiens (human) / References: UniProt: A0A7H0DNC0
#4: Protein Uracil-DNA glycosylase / UDG


Mass: 25107.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG116, UNG, MPXVgp099 / Production host: Homo sapiens (human) / References: UniProt: M1LL92, uracil-DNA glycosylase

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DNA chain / Non-polymers , 2 types, 2 molecules T

#5: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 8776.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Monkeypox virus
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Source: (synth.) Monkeypox virus / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MPXV replisome / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56874 / Symmetry type: POINT

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