9L8U | pdb_00009l8u

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

• PDB DOI: https://doi.org/10.2210/pdb9L8U/pdb
• 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

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

Hu, Z., Yan, R.

To be published.

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