5ZXV

Structural definition of a unique neutralization epitope on the receptor-binding domain of MERS-CoV spike glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.482 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.307 

wwPDB Validation 3D Report Full Report


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Literature

Structural Definition of a Unique Neutralization Epitope on the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein

Zhang, S.Zhou, P.Wang, P.Li, Y.Jiang, L.Jia, W.Wang, H.Fan, A.Wang, D.Shi, X.Fang, X.Hammel, M.Wang, S.Wang, X.Zhang, L.

(2018) Cell Rep 24: 441-452

  • DOI: 10.1016/j.celrep.2018.06.041
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The major mechanism of antibody-mediated neutralization of the Middle East respiratory syndrome coronavirus (MERS-CoV) involves competition with the cellular receptor dipeptidyl peptidase 4 (DPP4) for binding to the receptor-binding domain (RBD) of t ...

    The major mechanism of antibody-mediated neutralization of the Middle East respiratory syndrome coronavirus (MERS-CoV) involves competition with the cellular receptor dipeptidyl peptidase 4 (DPP4) for binding to the receptor-binding domain (RBD) of the spike (S) glycoprotein. Here, we report a unique epitope and unusual neutralizing mechanism of the isolated human antibody MERS-4. Structurally, MERS-4 approached the RBD from the outside of the RBD-DPP4 binding interface. Such binding resulted in the folding of the β5-β6 loop toward a shallow groove on the RBD interface critical for accommodating DPP4. The key residues for binding are identified through site-directed mutagenesis. Structural modeling revealed that MERS-4 binds to RBD only in the "up" position in the S trimer. Furthermore, MERS-4 demonstrated synergy with several reported antibodies. These results indicate that MERS-4 neutralizes MERS-CoV by indirect rather than direct competition with DPP4. This mechanism provides a valuable addition for the combined use of antibodies against MERS-CoV infection.


    Organizational Affiliation

    The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MERS-CoV RBD
A, B
208Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)Mutation(s): 0 
Gene Names: S
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Go to UniProtKB:  K9N5Q8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
heavy chain
H, C
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
light chain
L, D
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.482 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.307 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 138.647α = 90.00
b = 138.647β = 90.00
c = 228.736γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-05-21 
  • Released Date: 2018-07-25 
  • Deposition Author(s): Zhang, S., Wang, X.

Funding OrganizationLocationGrant Number
China--

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release