Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.22 kDa 
• Atom Count: 3492 
• Modelled Residue Count: 445 
• Deposited Residue Count: 445 
• Unique protein chains: 1

5K6H

Crystal structure of prefusion-stabilized RSV F single-chain 9-10 DS-Cav1 A149C-Y458C variant.

• PDB DOI: 10.2210/pdb5K6H/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human respiratory syncytial virus A2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-05-24 Released: 2016-09-21 
• Deposition Author(s): Joyce, M.G., Zhang, B., Mascola, J.R., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.252 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Literature

Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV.

Joyce, M.G., Zhang, B., Ou, L., Chen, M., Chuang, G.Y., Druz, A., Kong, W.P., Lai, Y.T., Rundlet, E.J., Tsybovsky, Y., Yang, Y., Georgiev, I.S., Guttman, M., Lees, C.R., Pancera, M., Sastry, M., Soto, C., Stewart-Jones, G.B., Thomas, P.V., Van Galen, J.G., Baxa, U., Lee, K.K., Mascola, J.R., Graham, B.S., Kwong, P.D.

(2016) Nat Struct Mol Biol 23: 811-820

• PubMed: 27478931 
• DOI: 10.1038/nsmb.3267
• Primary Citation of Related Structures:  
  5K6B, 5K6C, 5K6F, 5K6G, 5K6H, 5K6I


• PubMed Abstract: 
  

Structure-based design of vaccines, particularly the iterative optimization used so successfully in the structure-based design of drugs, has been a long-sought goal. We previously developed a first-generation vaccine antigen called DS-Cav1, comprising a prefusion-stabilized form of the fusion (F) glycoprotein, which elicits high-titer protective responses against respiratory syncytial virus (RSV) in mice and macaques. Here we report the improvement of DS-Cav1 through iterative cycles of structure-based design that significantly increased the titer of RSV-protective responses. The resultant second-generation 'DS2'-stabilized immunogens have their F subunits genetically linked, their fusion peptides deleted and their interprotomer movements stabilized by an additional disulfide bond. These DS2 immunogens are promising vaccine candidates with superior attributes, such as their lack of a requirement for furin cleavage and their increased antigenic stability against heat inactivation. The iterative structure-based improvement described here may have utility in the optimization of other vaccine antigens.

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Organizational Affiliation: 

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A [auth F]	445	Human respiratory syncytial virus A2	Mutation(s): 10  Gene Names: F
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.252 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.082	α = 90
b = 169.082	β = 90
c = 169.082	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-24 
• Released Date: 2016-09-21 
Deposition Author(s): Joyce, M.G., Zhang, B., Mascola, J.R., Kwong, P.D.

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release