9JA3 | pdb_00009ja3

Herpes simplex virus type 1 polymerase machinery in complex with duplex DNA, acyclovir triphosphate and calcium ions

• PDB DOI: https://doi.org/10.2210/pdb9JA3/pdb
• NAKB: 9JA3
• EM Map EMD-61289: EMDB EMDataResource

• Classification: REPLICATION
• Organism(s): Human alphaherpesvirus 1 strain 17, synthetic construct
• Expression System: Insect expression vector pBlueBacmsGCA1, Insect expression vector pBlueBacmsGCA1His
• Mutation(s): No 


• Deposited: 2024-08-24 Released: 2025-09-03 
• Deposition Author(s): Wu, Y.Q., Chen, X.L., Jiang, Z.Y., Li, D.Y., Zhang, Z.Y., Dong, C.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of herpes simplex type 1 virus DNA polymerase holoenzyme in DNA replication and acyclovir inhibition and proof-reading

Wu, Y.Q., Chen, X.L., Jiang, Z.Y., Li, D.Y., Zhang, Z.Y., Dong, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 206.9 kDa 
• Atom Count: 11,493 
• Modeled Residue Count: 1,399 
• Deposited Residue Count: 1,798 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	1,235	Human alphaherpesvirus 1 strain 17	Mutation(s): 0  Gene Names: UL30 EC: 2.7.7.7 (PDB Primary Data), 3.1.26.4 (UniProt)
UniProt
Find proteins for P04293 (Human herpesvirus 1 (strain 17)) Explore P04293  Go to UniProtKB:  P04293

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase processivity factor	B	513	Human alphaherpesvirus 1 strain 17	Mutation(s): 0  Gene Names: UL42
UniProt
Find proteins for P10226 (Human herpesvirus 1 (strain 17)) Explore P10226  Go to UniProtKB:  P10226

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	C [auth T]	27	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*CP*CP*AP*TP*AP*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')	D [auth P]	23	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AVP (Subject of Investigation/LOI)	H [auth T]	ACYCLOVIR TRIPHOSPHATE C8 H14 N5 O12 P3 AYWLSIKEOSXJLA-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Wu, Y.Q., Chen, X.L., Jiang, Z.Y., Li, D.Y., Zhang, Z.Y., Dong, C.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32250710142

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release