9OAL | pdb_00009oal

Cryo-EM structure of EBV gB prefusion construct C3-GT

PDB DOI: https://doi.org/10.2210/pdb9OAL/pdb
EM Map EMD-70288: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): human gammaherpesvirus 4
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-04-21 Released: 2025-12-31
Deposition Author(s): McCool, R.S., McLellan, J.S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Design, Structure, and Immunogenicity of a Soluble Prefusion-stabilized EBV gB Antigen.

McCool, R.S., Acreman, C.A., Powell, A.E., Picucci, S.I., Stieh, D.J., Huynh, J., Caruso, H., Park, S., Chen, J.-L., O'Rear, J., Palanski, B.A., Byrne, P.O., Sponholtz, M.R., Chou, C.-W., Ledgerwood, J.E., Weidenbacher, P.A.-B., McLellan, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 259.68 kDa
Atom Count: 13,059
Modeled Residue Count: 1,620
Deposited Residue Count: 2,325
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein B	A, B, C	775	human gammaherpesvirus 4	Mutation(s): 17 Gene Names: gB, BALF4
UniProt
Find proteins for P0C762 (Epstein-Barr virus (strain GD1)) Explore P0C762 Go to UniProtKB: P0C762
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C762
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F	3		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Coot
MODEL REFINEMENT	ISOLDE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-12-31
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.