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- PDB-9l8t: The apo structure (State 1) of African Swine Fever Virus DNA poly... -

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Basic information

Entry
Database: PDB / ID: 9l8t
TitleThe apo structure (State 1) of African Swine Fever Virus DNA polymerase
ComponentsDNA polymerase
KeywordsDNA BINDING PROTEIN / ASFV / DNA polymerase / Virus
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
Biological speciesAfrican swine fever virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)115,2581
Polymers115,2581
Non-polymers00
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

#1: Protein DNA polymerase


Mass: 115258.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Production host: Eukaryota (eukaryotes)
References: UniProt: A0A7D5JBM0, DNA-directed DNA polymerase
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 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Asfarviridae (virus)
Source (recombinant)Organism: Eukaryota (eukaryotes)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
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 magnification: 105000 X / 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 / Alignment procedure: BASIC
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) / Num. of grids imaged: 2 / Num. of real images: 2626
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277489 / Symmetry type: POINT
RefinementHighest resolution: 2.92 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038299
ELECTRON MICROSCOPYf_angle_d0.58811222
ELECTRON MICROSCOPYf_dihedral_angle_d4.411099
ELECTRON MICROSCOPYf_chiral_restr0.0421209
ELECTRON MICROSCOPYf_plane_restr0.0041437

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