4MMS

Crystal Structure of Prefusion-stabilized RSV F Variant Cav1 at pH 5.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus.

McLellan, J.S.Chen, M.Joyce, M.G.Sastry, M.Stewart-Jones, G.B.Yang, Y.Zhang, B.Chen, L.Srivatsan, S.Zheng, A.Zhou, T.Graepel, K.W.Kumar, A.Moin, S.Boyington, J.C.Chuang, G.Y.Soto, C.Baxa, U.Bakker, A.Q.Spits, H.Beaumont, T.Zheng, Z.Xia, N.Ko, S.Y.Todd, J.P.Rao, S.Graham, B.S.Kwong, P.D.

(2013) Science 342: 592-598

  • DOI: https://doi.org/10.1126/science.1243283
  • Primary Citation of Related Structures:  
    4MMQ, 4MMR, 4MMS, 4MMT, 4MMU, 4MMV

  • PubMed Abstract: 

    Respiratory syncytial virus (RSV) is the leading cause of hospitalization for children under 5 years of age. We sought to engineer a viral antigen that provides greater protection than currently available vaccines and focused on antigenic site Ø, a metastable site specific to the prefusion state of the RSV fusion (F) glycoprotein, as this site is targeted by extremely potent RSV-neutralizing antibodies. Structure-based design yielded stabilized versions of RSV F that maintained antigenic site Ø when exposed to extremes of pH, osmolality, and temperature. Six RSV F crystal structures provided atomic-level data on how introduced cysteine residues and filled hydrophobic cavities improved stability. Immunization with site Ø-stabilized variants of RSV F in mice and macaques elicited levels of RSV-specific neutralizing activity many times the protective threshold.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion glycoprotein F2
A, C, E
82Human respiratory syncytial virus A2Mutation(s): 1 
Gene Names: F
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2))
Explore P03420 
Go to UniProtKB:  P03420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03420
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion glycoprotein F1 fused with Fibritin trimerization domain
B, D, F
414Human respiratory syncytial virus A2Tequatrovirus T4
This entity is chimeric
Mutation(s): 5 
Gene Names: F
UniProt
Find proteins for P10104 (Enterobacteria phage T4)
Explore P10104 
Go to UniProtKB:  P10104
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2))
Explore P03420 
Go to UniProtKB:  P03420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP03420P10104
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
I [auth B]
J [auth B]
K [auth B]
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth D],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth F],
R [auth F],
S [auth F],
T [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.753α = 90
b = 170.753β = 90
c = 163.89γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.2: 2017-09-20
    Changes: Database references
  • Version 1.3: 2021-06-02
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description