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- PDB-9l8u: Cryo-EM structure of ASFV DNA polymerase in a DNA replication state -

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Basic information

Entry
Database: PDB / ID: 9l8u
TitleCryo-EM structure of ASFV DNA polymerase in a DNA replication state
Components
  • DNA (5'-D(P*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3')
  • DNA polymerase
KeywordsDNA BINDING PROTEIN/DNA / Virus / DNA polymerase / ASFV / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


viral DNA genome replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / DNA binding
Similarity search - Function
: / DNA polymerase family B, thumb domain / 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 polymerase family B, thumb domain / 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
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesAsfarviridae (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsHu, Z. / Yan, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: iScience / Year: 2025
Title: Structural basis for DNA replication by the African swine fever virus polymerase.
Authors: Ziwei Hu / Yongjie SunKang / Zhiheng Liu / Lihong Huang / Wenbao Qi / Renhong Yan /
Abstract: African swine fever virus (ASFV) devastates swine herds and lacks widely available antivirals. We show that the ASFV DNA polymerase beta (Pol β; gene ) localizes to viral replication factories and ...African swine fever virus (ASFV) devastates swine herds and lacks widely available antivirals. We show that the ASFV DNA polymerase beta (Pol β; gene ) localizes to viral replication factories and is required for viral replication. Cryo-electron microscopy structures of Pol β in apo and double-stranded DNA (dsDNA)-bound states reveal pronounced conformational flexibility that enables transitions between functional states. Binding to dsDNA promotes higher-order oligomerization that is essential for catalytic activity, as demonstrated by structure-guided mutagenesis and biochemical assays. These findings define the structural basis of ASFV genome synthesis, highlight the functional significance of Pol β during viral replication, and provide a framework for polymerase-targeted antiviral discovery.
History
DepositionDec 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jan 28, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 2.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
B: DNA (5'-D(P*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3')
C: DNA (5'-D(P*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4067
Polymers123,4233
Non-polymers9834
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein DNA polymerase


Mass: 115127.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Asfarviridae' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A7D5JBM0.
Source: (gene. exp.) Asfarviridae (virus) / Gene: G1211R / Production host: Eukaryota (eukaryotes)
References: UniProt: A0A7D5JBM0, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3')


Mass: 5067.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asfarviridae (virus) / Production host: Eukaryota (eukaryotes)
#3: DNA chain DNA (5'-D(P*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*A)-3')


Mass: 3229.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asfarviridae (virus) / Production host: Eukaryota (eukaryotes)
#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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: ASFV DNA polymerase with dsDNA / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Asfarviridae (virus)
Source (recombinant)Organism: Eukaryota (eukaryotes)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm / Calibrated defocus min: 1400 nm / Calibrated defocus max: 1800 nm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.5625 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 696619 / Symmetry type: POINT

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