Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 226.96 kDa 
• Atom Count: 13999 
• Modelled Residue Count: 1806 
• Deposited Residue Count: 2043 
• Unique protein chains: 2

5TOK

Crystal structure of the RSV F glycoprotein in complex with the neutralizing single-domain antibody F-VHH-L66

• PDB DOI: 10.2210/pdb5TOK/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human orthopneumovirus, Lama glama
• Expression System: Homo sapiens, Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2016-10-17 Released: 2017-02-22 
• Deposition Author(s): Gilman, M.S.A., Kabeche, S.C., McLellan, J.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), IWT-Vlaanderen, FWO-Vlaanderen, Ghent University, Interuniversity Attraction Poles Program, VIB and Mineco

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.286 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 

Literature

Potent single-domain antibodies that arrest respiratory syncytial virus fusion protein in its prefusion state.

Rossey, I., Gilman, M.S., Kabeche, S.C., Sedeyn, K., Wrapp, D., Kanekiyo, M., Chen, M., Mas, V., Spitaels, J., Melero, J.A., Graham, B.S., Schepens, B., McLellan, J.S., Saelens, X.

(2017) Nat Commun 8: 14158-14158

• PubMed: 28194013 
• DOI: 10.1038/ncomms14158
• Primary Citation of Related Structures:  
  5TOJ, 5TOK, 5TP3


• PubMed Abstract: 
  

Human respiratory syncytial virus (RSV) is the main cause of lower respiratory tract infections in young children. The RSV fusion protein (F) is highly conserved and is the only viral membrane protein that is essential for infection. The prefusion conformation of RSV F is considered the most relevant target for antiviral strategies because it is the fusion-competent form of the protein and the primary target of neutralizing activity present in human serum. Here, we describe two llama-derived single-domain antibodies (VHHs) that have potent RSV-neutralizing activity and bind selectively to prefusion RSV F with picomolar affinity. Crystal structures of these VHHs in complex with prefusion F show that they recognize a conserved cavity formed by two F protomers. In addition, the VHHs prevent RSV replication and lung infiltration of inflammatory monocytes and T cells in RSV-challenged mice. These prefusion F-specific VHHs represent promising antiviral agents against RSV.

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Organizational Affiliation: 

Department of Biomedical Molecular Biology, Ghent University, Ghent B-9052, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0, Fibritin chimera	A, B, C	550	Human orthopneumovirus	Mutation(s): 6
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
Single-domain antibody F-VHH-L66	D, E, F	131	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth B], J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.286 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 
• Space Group: P 3₁ 2 1
• Diffraction Data DOI: 10.15785/SBGRID/427 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.89	α = 90
b = 138.89	β = 90
c = 221.902	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-17 
• Released Date: 2017-02-22 
Deposition Author(s): Gilman, M.S.A., Kabeche, S.C., McLellan, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008704
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM113132
IWT-Vlaanderen	Belgium	Ph.D. Student Fellowship
FWO-Vlaanderen	Belgium	Postdoctoral Fellowship
Ghent University	Belgium	BOF12/GOA/014
Interuniversity Attraction Poles Program	Belgium	IAP7, BELVIR
VIB and Mineco	Spain	SAF2015-67033-R

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Database references
• Version 1.2: 2017-04-26
  Changes: Experimental preparation
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary