6J11

MERS-CoV spike N-terminal domain and 7D10 scFv complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report



Literature

Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein.

Zhou, H.Chen, Y.Zhang, S.Niu, P.Qin, K.Jia, W.Huang, B.Zhang, S.Lan, J.Zhang, L.Tan, W.Wang, X.

(2019) Nat Commun 10: 3068-3068

  • DOI: 10.1038/s41467-019-10897-4
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). The epitopes ...

    Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). The epitopes and mechanisms of mAbs targeting non-RBD regions have not been well characterized yet. Here we report the monoclonal antibody 7D10 that binds to the N-terminal domain (NTD) of the spike glycoprotein and inhibits the cell entry of MERS-CoV with high potency. Structure determination and mutagenesis experiments reveal the epitope and critical residues on the NTD for 7D10 binding and neutralization. Further experiments indicate that the neutralization by 7D10 is not solely dependent on the inhibition of DPP4 binding, but also acts after viral cell attachment, inhibiting the pre-fusion to post-fusion conformational change of the spike. These properties give 7D10 a wide neutralization breadth and help explain its synergistic effects with several RBD-targeting antibodies.


    Organizational Affiliation

    Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, 610065, Chengdu, China. xinquanwang@mail.tsinghua.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-terminal domain of Spike glycoprotein
A, B, C
336Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: S
Find proteins for A0A2D0YPK3 (Middle East respiratory syndrome-related coronavirus)
Go to UniProtKB:  A0A2D0YPK3

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VH of 7D10
D, F, H
132Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VL of 7D10
E, G, L
111Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A, B, C, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A, B, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.571α = 90
b = 180.355β = 90
c = 245.157γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFD0500307
Ministry of Science and Technology (China)China2016YFD0500301

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release