9YCV | pdb_00009ycv

HSV Helicase-primase complex bound to amenamevir

• PDB DOI: https://doi.org/10.2210/pdb9YCV/pdb
• EM Map EMD-72789: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human alphaherpesvirus 1 strain R-15
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-09-19 Released: 2025-12-31 
• Deposition Author(s): Yu, Z., Abraham, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanisms of HSV replisome assembly and targeting by helicase?primase inhibitors

Yu, Z., Abraham, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 295.72 kDa 
• Atom Count: 17,299 
• Modeled Residue Count: 2,222 
• Deposited Residue Count: 2,696 
• Unique protein chains: 3
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UL52	B [auth C]	1,058	Human alphaherpesvirus 1 strain R-15	Mutation(s): 0  Gene Names: UL52
UniProt
Find proteins for A0A5J6DWG4 (Human herpesvirus 1) Explore A0A5J6DWG4  Go to UniProtKB:  A0A5J6DWG4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UL5	C [auth A]	882	Human alphaherpesvirus 1 strain R-15	Mutation(s): 0  Gene Names: UL5
UniProt
Find proteins for A0A5J6DVR7 (Human herpesvirus 1) Explore A0A5J6DVR7  Go to UniProtKB:  A0A5J6DVR7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
UL8	D [auth B]	750	Human alphaherpesvirus 1 strain R-15	Mutation(s): 0  Gene Names: UL8
UniProt
Find proteins for P10192 (Human herpesvirus 1 (strain 17)) Explore P10192  Go to UniProtKB:  P10192

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')	A [auth D]	6	Human alphaherpesvirus 1 strain R-15

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BXD (Subject of Investigation/LOI)	F [auth A]	Amenamevir C24 H26 N4 O5 S MNHNIVNAFBSLLX-UHFFFAOYSA-N
ZN	E [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 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): Yu, Z., Abraham, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release