6PXH

Crystal Structure of MERS-CoV S1-NTD bound with G2 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD.

Wang, N.Rosen, O.Wang, L.Turner, H.L.Stevens, L.J.Corbett, K.S.Bowman, C.A.Pallesen, J.Shi, W.Zhang, Y.Leung, K.Kirchdoerfer, R.N.Becker, M.M.Denison, M.R.Chappell, J.D.Ward, A.B.Graham, B.S.McLellan, J.S.

(2019) Cell Rep 28: 3395-3405.e6

  • DOI: 10.1016/j.celrep.2019.08.052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) p ...

    Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) protein have been characterized, but much less is known about antibodies targeting non-RBD epitopes. Here, we report the structural and functional characterization of G2, a neutralizing antibody targeting the MERS-CoV S1 N-terminal domain (S1-NTD). Structures of G2 alone and in complex with the MERS-CoV S1-NTD define a site of vulnerability comprising two loops, each of which contain a residue mutated in G2-escape variants. Cell-surface binding studies and in vitro competition experiments demonstrate that G2 strongly disrupts the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4), with the inhibition requiring the native trimeric S conformation. These results advance our understanding of antibody-mediated neutralization of coronaviruses and should facilitate the development of immunotherapeutics and vaccines against MERS-CoV.


    Organizational Affiliation

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA. Electronic address: jmclellan@austin.utexas.edu.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MERS-CoV S1-NTD
A, B
342Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: S
Find proteins for V9TWK2 (Middle East respiratory syndrome-related coronavirus)
Go to UniProtKB:  V9TWK2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
G2 heavy chain
C, H
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
G2 light chain
D, L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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

Download SDF File 
Download CCD File 
A, B
DIHYDROFOLIC ACID
C19 H21 N7 O6
OZRNSSUDZOLUSN-LBPRGKRZSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.989α = 90.00
b = 63.860β = 90.75
c = 186.778γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01AI127521

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references