8W3J | pdb_00008w3j

Crystal structure of prefusion-stabilized RSV F protein UFCR2-iSS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 
    0.258 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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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

  • DOI: https://doi.org/10.1038/s41467-024-54287-x
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prefusion-stabilized RSV F protein UFCR2-iSSA [auth F]507Human respiratory syncytial virus A2Mutation(s): 0 
UniProt
Find proteins for G3C7N1 (Human respiratory syncytial virus)
Explore G3C7N1 
Go to UniProtKB:  G3C7N1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3C7N1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free:  0.258 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.22α = 90
b = 169.22β = 90
c = 169.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

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