5VZR

Crystal Structure of MERS-CoV neutralizing antibody G4 Fab

  • Classification: IMMUNE SYSTEM
  • Expression System: Homo sapiens

  • Deposited: 2017-05-29 Released: 2017-08-30 
  • Deposition Author(s): Wang, N., Wrapp, D., McLellan, J.S.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen.

Pallesen, J.Wang, N.Corbett, K.S.Wrapp, D.Kirchdoerfer, R.N.Turner, H.L.Cottrell, C.A.Becker, M.M.Wang, L.Shi, W.Kong, W.P.Andres, E.L.Kettenbach, A.N.Denison, M.R.Chappell, J.D.Graham, B.S.Ward, A.B.McLellan, J.S.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E7348-E7357

  • DOI: 10.1073/pnas.1707304114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein ...

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232.,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037; Nianshuang.Wang@dartmouth.edu andrew@scripps.edu Jason.S.McLellan@Dartmouth.edu.,Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755; Nianshuang.Wang@dartmouth.edu andrew@scripps.edu Jason.S.McLellan@Dartmouth.edu.,Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892.,Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755.,Virology Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
G4 antibody heavy chain
H, A
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
G4 antibody light chain
L, B
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, H
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 80.678α = 90.00
b = 88.759β = 90.00
c = 128.469γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI127521

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence
  • Version 2.0: 2019-12-11
    Type: Author supporting evidence, Polymer sequence