5U68 | pdb_00005u68

Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus

• PDB DOI: https://doi.org/10.2210/pdb5U68/pdb

• Classification: VIRAL PROTEIN/Immune System
• Organism(s): Human respiratory syncytial virus A2, Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-12-07 Released: 2017-02-15 
• Deposition Author(s): Wen, X., Jardetzky, T.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Models: experimental

Literature

Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus.

Wen, X., Mousa, J.J., Bates, J.T., Lamb, R.A., Crowe, J.E., Jardetzky, T.S.

(2017) Nat Microbiol 2: 16272-16272

• PubMed: 28134915 
• DOI: https://doi.org/10.1038/nmicrobiol.2016.272
• Primary Citation Related Structures: 
  5U68


• PubMed Abstract: 
  

  Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are two closely related viruses that cause bronchiolitis and pneumonia in infants and the elderly ¹ , with a significant health burden ^2-6 . There are no licensed vaccines or small-molecule antiviral treatments specific to these two viruses at present. A humanized murine monoclonal antibody (palivizumab) is approved to treat high-risk infants for RSV infection ^7,8 , but other treatments, as well as vaccines, for both viruses are still in development. Recent epidemiological modelling suggests that cross-immunity between RSV, HMPV and human parainfluenzaviruses may contribute to their periodic outbreaks ⁹ , suggesting that a deeper understanding of host immunity to these viruses may lead to enhanced strategies for their control. Cross-reactive neutralizing antibodies to the RSV and HMPV fusion (F) proteins have been identified ^10,11 . Here, we examine the structural basis for cross-reactive antibody binding to RSV and HMPV F protein by two related, independently isolated antibodies, MPE8 and 25P13. We solved the structure of the MPE8 antibody bound to RSV F protein and identified the 25P13 antibody from an independent blood donor. Our results indicate that both antibodies use germline residues to interact with a conserved surface on F protein that could guide the emergence of cross-reactivity. The induction of similar cross-reactive neutralizing antibodies using structural vaccinology approaches could enhance intrinsic cross-immunity to these paramyxoviruses and approaches to controlling recurring outbreaks.

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Organizational Affiliation: 
• Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
Vanderbilt Vaccine Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois 60208-3500, USA.
Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA.
Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 279.41 kDa 
• Atom Count: 15,642 
• Modeled Residue Count: 2,043 
• Deposited Residue Count: 2,568 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera protein of Fusion glycoprotein F0 and Envelope glycoprotein	A, B, C	562	Human respiratory syncytial virus A2, Human immunodeficiency virus 1 This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for M1E1E4 (Human immunodeficiency virus type 1) Explore M1E1E4  Go to UniProtKB:  M1E1E4
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420
UniProt Groups	M1E1E4P03420

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MPE8	D [auth E], E [auth F], F [auth G]	294	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.54	α = 90
b = 155.54	β = 90
c = 275.93	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Wen, X., Jardetzky, T.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-61050

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Source and taxonomy
• Version 1.2: 2017-08-09
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence
• Version 1.5: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary