9OEF | pdb_00009oef

Structure of the human astrovirus VA1 capsid spike bound to antibody 7C8

PDB DOI: https://doi.org/10.2210/pdb9OEF/pdb
EM Map EMD-70397: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Astrovirus VA1, Mus musculus
Expression System: Escherichia coli, Cricetulus griseus
Mutation(s): No

Deposited: 2025-04-28 Released: 2026-07-08
Deposition Author(s): Ghosh, A., Dzimianski, J.V., Balasco Serrao, V.H., DuBois, R.M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9OEF

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

Literature

Cryo-EM Structures of the Human Astrovirus VA1 Capsid Spike Bound to Neutralizing Antibodies: Implications for Therapeutic Strategies

Ghosh, A., Dzimianski, J.V., Lopez, T., Espinosa, R., Balasco Serrao, V.H., Arias, C.F., DuBois, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 158.3 kDa
Atom Count: 7,148
Modeled Residue Count: 908
Deposited Residue Count: 1,446
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein VP38	A [auth C], D [auth A]	289	Astrovirus VA1	Mutation(s): 0 Gene Names: ORF2
UniProt
Find proteins for C7BG48 (Human astrovirus VA1) Explore C7BG48 Go to UniProtKB: C7BG48
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7BG48
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
7C8 heavy chain	B [auth H], E [auth J]	219	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
7C8 light chain	C [auth L], F [auth K]	215	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	PHENIX	1.21.2-5419

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-08

Deposition Author(s):

Dzimianski, J.V.

Balasco Serrao, V.H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI144090

Revision History (Full details and data files)

Version 1.0: 2026-07-08
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.