6OE4 | pdb_00006oe4

Prefusion RSV F monomer bound by neutralizing antibody CR9501

• PDB DOI: https://doi.org/10.2210/pdb6OE4/pdb

• Classification: Viral protein/immune system
• Organism(s): Human respiratory syncytial virus A2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2019-03-27 Released: 2019-04-17 
• Deposition Author(s): McLellan, J.S., Gilman, M.S.A.
• 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: 3.30 Å
• R-Value Free: 
  0.259 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Transient opening of trimeric prefusion RSV F proteins.

Gilman, M.S.A., Furmanova-Hollenstein, P., Pascual, G., B van 't Wout, A., Langedijk, J.P.M., McLellan, J.S.

(2019) Nat Commun 10: 2105-2105

• PubMed: 31068578 
• DOI: https://doi.org/10.1038/s41467-019-09807-5
• Primary Citation Related Structures: 
  6OE4, 6OE5


• PubMed Abstract: 
  

  The respiratory syncytial virus (RSV) F glycoprotein is a class I fusion protein that mediates viral entry and is a major target of neutralizing antibodies. Structures of prefusion forms of RSV F, as well as other class I fusion proteins, have revealed compact trimeric arrangements, yet whether these trimeric forms can transiently open remains unknown. Here, we perform structural and biochemical studies on a recently isolated antibody, CR9501, and demonstrate that it enhances the opening of prefusion-stabilized RSV F trimers. The 3.3 Å crystal structure of monomeric RSV F bound to CR9501, combined with analysis of over 25 previously determined RSV F structures, reveals a breathing motion of the prefusion conformation. We also demonstrate that full-length RSV F trimers transiently open and dissociate on the cell surface. Collectively, these findings have implications for the function of class I fusion proteins, as well as antibody prophylaxis and vaccine development for RSV.

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Organizational Affiliation: 
• Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
Janssen Infectious Diseases and Vaccines, Leiden, CN, 2333, The Netherlands.
Janssen Immunosciences, World Without Disease Accelerator, San Diego, CA, 92121, USA.
Janssen Prevention Center, Janssen Vaccines & Prevention B.V, Leiden, CN, 2333, The Netherlands.
AlphaBiomics, London, SW4 0PA, United Kingdom.
Janssen Infectious Diseases and Vaccines, Leiden, CN, 2333, The Netherlands. [e-mail].
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 212.05 kDa 
• Atom Count: 13,310 
• Modeled Residue Count: 1,732 
• Deposited Residue Count: 1,930 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B [auth D]	521	Human respiratory syncytial virus A2	Mutation(s): 4
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CR9501 Fab Light Chain	C, F	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CR9501 Fab Heavy Chain	D [auth B], E	230	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth D], H [auth C], I [auth C], J [auth F], K [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.259 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.628	α = 90
b = 153.389	β = 90
c = 155.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): McLellan, J.S., Gilman, M.S.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008704

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Refinement description, Structure summary