Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 299049.69 
• Atom Count: 19902 
• Residue Count: 2727 
• Unique protein chains: 4

5J3D

Crystal structure of human Fab 14N4 in complex with post-fusion RSV F

• DOI: 10.2210/pdb5J3D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human respiratory syncytial virus A (strain A2)
• Expression System: Homo sapiens


• Deposited: 2016-03-30 Released: 2016-10-26 
• Deposition Author(s): Mousa, J.J., Crowe, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.077 Å
• R-Value Free: 0.282 
• R-Value Work: 0.257 

Literature

Structural basis for nonneutralizing antibody competition at antigenic site II of the respiratory syncytial virus fusion protein.

Mousa, J.J., Sauer, M.F., Sevy, A.M., Finn, J.A., Bates, J.T., Alvarado, G., King, H.G., Loerinc, L.B., Fong, R.H., Doranz, B.J., Correia, B.E., Kalyuzhniy, O., Wen, X., Jardetzky, T.S., Schief, W.R., Ohi, M.D., Meiler, J., Crowe, J.E.

(2016) Proc.Natl.Acad.Sci.USA 113: E6849-E6858

• PubMed: 27791117 
• DOI: 10.1073/pnas.1609449113
• Primary Citation of Related Structures:  
  5ITB


• PubMed Abstract: 
  

Palivizumab was the first antiviral monoclonal antibody (mAb) approved for therapeutic use in humans, and remains a prophylactic treatment for infants at risk for severe disease because of respiratory syncytial virus (RSV). Palivizumab is an engineered humanized version of a murine mAb targeting antigenic site II of the RSV fusion (F) protein, a key target in vaccine development. There are limited reported naturally occurring human mAbs to site II; therefore, the structural basis for human antibody recognition of this major antigenic site is poorly understood. Here, we describe a nonneutralizing class of site II-specific mAbs that competed for binding with palivizumab to postfusion RSV F protein. We also describe two classes of site II-specific neutralizing mAbs, one of which escaped competition with nonneutralizing mAbs. An X-ray crystal structure of the neutralizing mAb 14N4 in complex with F protein showed that the binding angle at which human neutralizing mAbs interact with antigenic site II determines whether or not nonneutralizing antibodies compete with their binding. Fine-mapping studies determined that nonneutralizing mAbs that interfere with binding of neutralizing mAbs recognize site II with a pose that facilitates binding to an epitope containing F surface residues on a neighboring protomer. Neutralizing antibodies, like motavizumab and a new mAb designated 3J20 that escape interference by the inhibiting mAbs, avoid such contact by binding at an angle that is shifted away from the nonneutralizing site. Furthermore, binding to rationally and computationally designed site II helix-loop-helix epitope-scaffold vaccines distinguished neutralizing from nonneutralizing site II antibodies.

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Organizational Affiliation: 

Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
14N4 heavy chain	A, C, H	224	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
14N4 light chain	B, D, L	218	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Fusion glycoprotein F0	E, G, J	73	Human respiratory syncytial virus A (strain A2)	Mutation(s): 0  Gene Names: F
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Go to UniProtKB:  P03420

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Fusion glycoprotein F0	F, I, K	394	Human respiratory syncytial virus A (strain A2)	Mutation(s): 0  Gene Names: F
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Go to UniProtKB:  P03420

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.077 Å
• R-Value Free: 0.282 
• R-Value Work: 0.257 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 235.130	α = 90.00
b = 235.130	β = 90.00
c = 220.142	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-30 
• Released Date: 2016-10-26 
• Deposition Author(s): Mousa, J.J., Crowe, J.E.

Revision History 

• Version 1.0: 2016-10-26
  Type: Initial release
• Version 1.1: 2016-11-23
  Type: Database references