9UT4 | pdb_00009ut4

The primase module of the helicase-primase complex from HHV1 bound with ssDNA and amenamevir

PDB DOI: https://doi.org/10.2210/pdb9UT4/pdb
EM Map EMD-64480: EMDB EMDataResource

Classification: REPLICATION
Organism(s): Saccharomyces cerevisiae S288C, Human alphaherpesvirus 1
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2025-05-02 Released: 2026-04-08
Deposition Author(s): Sato, K., Kise, Y., Hamada, K., Nureki, O., Sengoku, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.91 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UT4

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

Literature

The helicase-primase complex from HHV1 bound with ssDNA and amenamevir

Sato, K., Kise, Y., Hamada, K., Nureki, O., Sengoku, T.

To be published.

Macromolecule Content

Total Structure Weight: 226.25 kDa
Atom Count: 8,607
Modeled Residue Count: 1,138
Deposited Residue Count: 2,082
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3,DNA primase	A [auth B]	1,195	Saccharomyces cerevisiae S288C, Human alphaherpesvirus 1 This entity is chimeric	Mutation(s): 2 Gene Names: SMT3, YDR510W, D9719.15, UL52 EC: 2.7.7
UniProt
Find proteins for P10236 (Human herpesvirus 1 (strain 17)) Explore P10236 Go to UniProtKB: P10236
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306 Go to UniProtKB: Q12306
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q12306 P10236
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein	B [auth C]	887	Saccharomyces cerevisiae S288C, Human alphaherpesvirus 1 This entity is chimeric	Mutation(s): 2 Gene Names: SMT3, YDR510W, D9719.15, UL8
UniProt
Find proteins for P10192 (Human herpesvirus 1 (strain 17)) Explore P10192 Go to UniProtKB: P10192
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306 Go to UniProtKB: Q12306
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q12306 P10192
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.91 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2026-04-08
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.