9YVG | pdb_00009yvg

Cryo-EM structure of BA.5 spike, Open conformation

PDB DOI: https://doi.org/10.2210/pdb9YVG/pdb
EM Map EMD-73523: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Homo
Mutation(s): No

Deposited: 2025-10-23 Released: 2026-08-26
Deposition Author(s): Ye, G., Bu, F., Li, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9YVG

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

Literature

A SARS-CoV-2 entry inhibitor trimerizes to lock the spike trimer in its closed conformation

Mou, H., Gao, B., Ye, G., Bu, F., Zhang, L., Farzan, M., Li, F., Choe, H.

To be published.

Macromolecule Content

Total Structure Weight: 420.84 kDa
Atom Count: 24,466
Modeled Residue Count: 3,098
Deposited Residue Count: 3,756
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,252	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 2	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	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E [auth I], F [auth M], G [auth N], H [auth O], D, E [auth I], F [auth M], G [auth N], H [auth O], I [auth P], J [auth Q], K [auth S], L [auth U]	2		N-Glycosylation	Interactions Focus chain D Focus chain E [auth I] Focus chain F [auth M] Focus chain G [auth N] Focus chain H [auth O] Focus chain I [auth P] Focus chain J [auth Q] Focus chain K [auth S] Focus chain L [auth U] Interactions & Density Focus chain D Focus chain E [auth I] Focus chain F [auth M] Focus chain G [auth N] Focus chain H [auth O] Focus chain I [auth P] Focus chain J [auth Q] Focus chain K [auth S] Focus chain L [auth U]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171954

Revision History (Full details and data files)

Version 1.0: 2026-08-26
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.