5TOK

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


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 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion glycoprotein F0, Fibritin chimeraA, B, C550Human orthopneumovirusMutation(s): 6 
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2))
Explore P03420 
Go to UniProtKB:  P03420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03420
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Single-domain antibody F-VHH-L66D, E, F131Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
J [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
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 = 138.89α = 90
b = 138.89β = 90
c = 221.902γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008704
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM113132
IWT-VlaanderenBelgiumPh.D. Student Fellowship
FWO-VlaanderenBelgiumPostdoctoral Fellowship
Ghent UniversityBelgiumBOF12/GOA/014
Interuniversity Attraction Poles ProgramBelgiumIAP7, BELVIR
VIB and MinecoSpainSAF2015-67033-R

Revision History  (Full details and data files)

  • 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