9NDA | pdb_00009nda

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

PDB DOI: https://doi.org/10.2210/pdb9NDA/pdb
EM Map EMD-49269: EMDB EMDataResource

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

Deposited: 2025-02-17 Released: 2025-08-13
Deposition Author(s): Yao, Q., Yu, X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure and Inhibition Mechanism of Herpesvirus Helicase-Primase

Yao, Q., Mercier, A.

To be published.

Macromolecule Content

Total Structure Weight: 194.13 kDa
Atom Count: 7,960
Modeled Residue Count: 1,044
Deposited Residue Count: 1,804
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase	A	1,057	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10236
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase/primase complex-associated protein	B [auth C]	747	Orthoherpesviridae	Mutation(s): 0 Gene Names: UL8
UniProt
Find proteins for P10192 (Human herpesvirus 1 (strain 17)) Explore P10192 Go to UniProtKB: P10192
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10192
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	United States	--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.