9E5V | pdb_00009e5v

The postfusion conformation of herpes simplex virus type 1 (HSV-1) glycoprotein B (gB)

PDB DOI: https://doi.org/10.2210/pdb9E5V/pdb
EM Map EMD-47529: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human alphaherpesvirus 1 strain F
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-10-28 Released: 2026-03-18
Deposition Author(s): Mou, Z., Wang, S., Dai, X.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9E5V

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

Literature

The prefusion conformation of herpes simplex virus type 1 (HSV-1) glycoprotein B (gB)

Mou, Z., Wang, S., Dai, X.

To be published.

Macromolecule Content

Total Structure Weight: 300.28 kDa
Atom Count: 14,319
Modeled Residue Count: 1,770
Deposited Residue Count: 2,688
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein B	A, B, C	896	Human alphaherpesvirus 1 strain F	Mutation(s): 1 Gene Names: gB, UL27
UniProt
Find proteins for P10211 (Human herpesvirus 1 (strain 17)) Explore P10211 Go to UniProtKB: P10211
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10211
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM151043

Revision History (Full details and data files)

Version 1.0: 2026-03-18
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.