4MMU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.228 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.6 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 F282Human 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 domain414Human respiratory syncytial virus A2Tequatrovirus T4
This entity is chimeric
Mutation(s): 7 
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
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.228 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.588α = 90
b = 168.588β = 90
c = 168.588γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

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: Data collection, Refinement description, Source and taxonomy
  • Version 1.2: 2017-09-20
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2021-06-02
    Changes: Source and taxonomy, Structure summary
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary