9LM5 | pdb_00009lm5

Cryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 strain: A2) in complex with nanobody 1G9

PDB DOI: https://doi.org/10.2210/pdb9LM5/pdb
EM Map EMD-63216: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Respiratory syncytial virus A2, Camelus bactrianus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-01-18 Released: 2026-01-21
Deposition Author(s): Wang, Q.Q., Ke, X.L., Li, E.T., Hong, D.X., Li, H.X., Cheng, Z.K., Zhang, J.C., Jin, T.C., Shu, B., Chiu, S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.77 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 strain: A2) in complex with nanobody 2A5

Wang, Q.Q., Ke, X.L., Li, E.T., Hong, D.X., Li, H.X., Cheng, Z.K., Zhang, J.C., Jin, T.C., Shu, B., Chiu, S.

To be published.

Macromolecule Content

Total Structure Weight: 234.26 kDa
Atom Count: 13,472
Modeled Residue Count: 1,755
Deposited Residue Count: 2,118
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B, C	569	Respiratory syncytial virus A2	Mutation(s): 3
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420 Go to UniProtKB: P03420
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03420
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody 1G9	D, E, F	137	Camelus bactrianus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.77 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-01-21
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.