9NEL | pdb_00009nel

The flexible portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex with amenamevir

• PDB DOI: https://doi.org/10.2210/pdb9NEL/pdb
• EM Map EMD-49326: EMDB EMDataResource

• Classification: REPLICATION, TRANSFERASE/INHIBITOR
• Organism(s): Orthoherpesviridae
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-02-19 Released: 2025-08-13 
• Deposition Author(s): Yao, Q., Yu, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and Inhibition Mechanism of Herpesvirus Helicase-Primase

Yao, Q., Mercier, A.

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: 209.84 kDa 
• Atom Count: 6,695 
• Modeled Residue Count: 847 
• Deposited Residue Count: 1,901 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase	A	1,058	Orthoherpesviridae	Mutation(s): 0  Gene Names: UL52 EC: 2.7.7
UniProt
Find proteins for P10236 (Human herpesvirus 1 (strain 17)) Explore P10236  Go to UniProtKB:  P10236

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication helicase	B	843	Orthoherpesviridae	Mutation(s): 0  Gene Names: HELI, UL5 EC: 3.6.4
UniProt
Find proteins for P10189 (Human herpesvirus 1 (strain 17)) Explore P10189  Go to UniProtKB:  P10189

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BXD (Subject of Investigation/LOI)	C [auth A]	Amenamevir C24 H26 N4 O5 S MNHNIVNAFBSLLX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Yao, Q., Yu, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release