9ZGF | pdb_00009zgf

The complex of HSV-1 proteins UL9 and ICP8 with forked DNA

• PDB DOI: https://doi.org/10.2210/pdb9ZGF/pdb
• EM Map EMD-74190: EMDB EMDataResource

• Classification: REPLICATION/DNA
• Organism(s): Human alphaherpesvirus 1 strain 17
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-02 Released: 2026-06-10 
• Deposition Author(s): Baranovskiy, A.G., Morstadt, L.M., Romero, E.E., Babayeva, N.D., Tahirov, T.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for unwinding the origins of HSV-1 genome by cooperative action of viral proteins UL9 and ICP8

Baranovskiy, A.G., Morstadt, L.M., Romero, E.E., Babayeva, N.D., Tahirov, T.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 245.24 kDa 
• Atom Count: 15,403 
• Modeled Residue Count: 1,896 
• Deposited Residue Count: 2,118 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major DNA-binding protein	A	1,196	Human alphaherpesvirus 1 strain 17	Mutation(s): 0  Gene Names: DBP, ICP8, UL29
UniProt
Find proteins for P04296 (Human herpesvirus 1 (strain 17)) Explore P04296  Go to UniProtKB:  P04296

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication origin-binding protein	B [auth C]	851	Human alphaherpesvirus 1 strain 17	Mutation(s): 0  Gene Names: UL9
UniProt
Find proteins for P10193 (Human herpesvirus 1 (strain 17)) Explore P10193  Go to UniProtKB:  P10193

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	C [auth D]	40	Human alphaherpesvirus 1 strain 17

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	D [auth E]	31	Human alphaherpesvirus 1 strain 17

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS (Subject of Investigation/LOI)	G [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-10 
Deposition Author(s): Baranovskiy, A.G., Morstadt, L.M., Romero, E.E., Babayeva, N.D., Tahirov, T.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM152032

Revision History  

• Version 1.0: 2026-06-10
  Type: Initial release