9L8U | pdb_00009l8u

Cryo-EM structure of ASFV DNA polymerase in a DNA replication state

• PDB DOI: https://doi.org/10.2210/pdb9L8U/pdb
• NAKB: 9L8U
• EM Map EMD-62891: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Asfarviridae
• Expression System: Eukaryota
• Mutation(s): No 


• Deposited: 2024-12-28 Released: 2025-12-31 
• Deposition Author(s): Hu, Z., Yan, R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.53 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for DNA replication by the African swine fever virus polymerase.

Hu, Z., SunKang, Y., Liu, Z., Huang, L., Qi, W., Yan, R.

(2025) iScience 28: 114155-114155

• PubMed: 41438038 
• DOI: https://doi.org/10.1016/j.isci.2025.114155
• Primary Citation of Related Structures:  
  9L8T, 9L8U


• PubMed 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 G1211R ) 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.

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Organizational Affiliation: 
• SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
African Swine Fever Regional Laboratory of China (Guangzhou), Guangzhou 510642, China.
Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China.
National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China.
Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 124.41 kDa 
• Atom Count: 8,649 
• Modeled Residue Count: 1,013 
• Deposited Residue Count: 1,019 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	992	Asfarviridae	Mutation(s): 0  Gene Names: G1211R EC: 2.7.7.7
UniProt
Find proteins for A0A7D5JBM0 (African swine fever virus) Explore A0A7D5JBM0  Go to UniProtKB:  A0A7D5JBM0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3')	B	16	Asfarviridae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*A)-3')	C	11	Asfarviridae

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	D [auth A], G [auth C]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.53 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Hu, Z., Yan, R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release
  
• Version 1.1: 2026-01-28
  Changes: Data collection, Database references