6W52

Prefusion RSV F bound by neutralizing antibody RSB1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.74 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


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


Literature

Convergent structural features of respiratory syncytial virus neutralizing antibodies and plasticity of the site V epitope on prefusion F.

Harshbarger, W., Tian, S., Wahome, N., Balsaraf, A., Bhattacharya, D., Jiang, D., Pandey, R., Tungare, K., Friedrich, K., Mehzabeen, N., Biancucci, M., Chinchilla-Olszar, D., Mallett, C.P., Huang, Y., Wang, Z., Bottomley, M.J., Malito, E., Chandramouli, S.

(2020) PLoS Pathog 16: e1008943-e1008943

  • DOI: 10.1371/journal.ppat.1008943
  • Primary Citation of Related Structures:  
    6W52, 6W5D

  • PubMed Abstract: 

    • Respiratory syncytial virus (RSV) is a global public health burden for which no licensed vaccine exists. To aid vaccine development via increased understanding of the protective antibody response to RSV prefusion glycoprotein F (PreF), we performed structural and functional studies using the human neutralizing antibody (nAb) RSB1 ...

    Respiratory syncytial virus (RSV) is a global public health burden for which no licensed vaccine exists. To aid vaccine development via increased understanding of the protective antibody response to RSV prefusion glycoprotein F (PreF), we performed structural and functional studies using the human neutralizing antibody (nAb) RSB1. The crystal structure of PreF complexed with RSB1 reveals a conformational, pre-fusion specific site V epitope with a unique cross-protomer binding mechanism. We identify shared structural features between nAbs RSB1 and CR9501, elucidating for the first time how diverse germlines obtained from different subjects can develop convergent molecular mechanisms for recognition of the same PreF site of vulnerability. Importantly, RSB1-like nAbs were induced upon immunization with PreF in naturally-primed cattle. Together, this work reveals new details underlying the immunogenicity of site V and further supports PreF-based vaccine development efforts.

    Organizational Affiliation: 

    GSK, Rockville, MD, United States of America.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion glycoprotein F0A82Human respiratory syncytial virus A2Mutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion glycoprotein F1 fused with Fibritin trimerization domainB414Human respiratory syncytial virus A, Escherichia phage T2
This entity is chimeric		Mutation(s): 0 
Gene Names: F, MZ07_64446gpF, wac
UniProt
Find proteins for Q76VI8 (Enterobacteria phage T2)
Explore Q76VI8 
Go to UniProtKB:  Q76VI8
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 GroupsQ76VI8P03420
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RSB1 Fab Heavy ChainC [auth H]283Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RSB1 Fab Light ChainD [auth L]236Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.74 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.225 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.298α = 90
b = 190.298β = 90
c = 190.298γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release