9ZW2 | pdb_00009zw2

HSV1 gB prefusion-2 trimers with "deliD" mutations

PDB DOI: https://doi.org/10.2210/pdb9ZW2/pdb
EM Map EMD-74903: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human alphaherpesvirus 1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-12-31 Released: 2026-11-04
Deposition Author(s): McCallum, M., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9ZW2

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

Literature

Prefusion- stabilization of the Herpesvirus fusion protein enhances vaccine potency

McCallum, M., Veesler, D.

To be published.

Macromolecule Content

Total Structure Weight: 495.47 kDa
Atom Count: 26,825
Modeled Residue Count: 3,492
Deposited Residue Count: 4,350
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HSV1 gB prefusion-2 trimers with "deliD" mutations	A, B, C, D, E A, B, C, D, E, F	725	Human alphaherpesvirus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L	3		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain BA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth F] CA [auth F] DA [auth F] M [auth A] AA [auth E], BA [auth F], CA [auth F], DA [auth F], M [auth A], N [auth A], O [auth A], P [auth B], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth C], V [auth D], W [auth D], X [auth D], Y [auth E], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release