8W3R | pdb_00008w3r

Crystal structure of prefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ in complex with A4 single-chain fragment variable

• PDB DOI: https://doi.org/10.2210/pdb8W3R/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2024-02-22 Released: 2025-01-15 
• Deposition Author(s): Lee, Y.Z., Stanfield, R.L., Wilson, I.A., Zhu, J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.02 Å
• R-Value Free: 
  0.303 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Literature

Rational design of uncleaved prefusion-closed trimer vaccines for human respiratory syncytial virus and metapneumovirus.

Lee, Y.Z., Han, J., Zhang, Y.N., Ward, G., Braz Gomes, K., Auclair, S., Stanfield, R.L., He, L., Wilson, I.A., Zhu, J.

(2024) Nat Commun 15: 9939-9939

• PubMed: 39550381 
• DOI: https://doi.org/10.1038/s41467-024-54287-x
• Primary Citation Related Structures: 
  8W3E, 8W3F, 8W3G, 8W3H, 8W3I, 8W3J, 8W3K, 8W3L, 8W3N, 8W3O, 8W3P, 8W3Q, 8W3R


• PubMed Abstract: 
  

  Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause human respiratory diseases and are major targets for vaccine development. In this study, we design uncleaved prefusion-closed (UFC) trimers for the fusion protein (F) of both viruses by examining mutations critical to F metastability. For RSV, we assess four previous prefusion F designs, including the first and second generations of DS-Cav1, SC-TM, and 847A. We then identify key mutations that can maintain prefusion F in a native-like, closed trimeric form (up to 76%) without introducing any interprotomer disulfide bond. For hMPV, we develop a stable UFC trimer with a truncated F ₂ -F ₁ linkage and an interprotomer disulfide bond. Dozens of UFC constructs are characterized by negative-stain electron microscopy (nsEM), x-ray crystallography (11 RSV-F structures and one hMPV-F structure), and antigenic profiling. Using an optimized RSV-F UFC trimer as bait, we identify three potent RSV neutralizing antibodies (NAbs) from a phage-displayed human antibody library, with a public NAb lineage targeting sites Ø and V and two cross-pneumovirus NAbs recognizing site III. In mouse immunization, rationally designed RSV-F and hMPV-F UFC trimers induce robust antibody responses with high neutralizing titers. Our study provides a foundation for future prefusion F-based RSV and hMPV vaccine development.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Uvax Bio, LLC, Newark, DE, 19702, USA.
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].
Uvax Bio, LLC, Newark, DE, 19702, USA. [e-mail].
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 84.2 kDa 
• Atom Count: 5,218 
• Modeled Residue Count: 681 
• Deposited Residue Count: 779 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A4 single-chain fragment variable	A	272	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
prefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ	B [auth F]	507	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for G3C7N1 (Human respiratory syncytial virus) Explore G3C7N1  Go to UniProtKB:  G3C7N1
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.02 Å
• R-Value Free:  0.303 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.24	α = 90
b = 100.24	β = 90
c = 588.218	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Lee, Y.Z., Stanfield, R.L., Wilson, I.A., Zhu, J.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release