5VZR | pdb_00005vzr

Crystal Structure of MERS-CoV neutralizing antibody G4 Fab

• PDB DOI: https://doi.org/10.2210/pdb5VZR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Models: experimental

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

• PubMed: 28807998 
• DOI: https://doi.org/10.1073/pnas.1707304114
• Primary Citation Related Structures: 
  5VYH, 5VZR, 5W9H, 5W9I, 5W9J, 5W9K, 5W9L, 5W9M, 5W9N, 5W9O, 5W9P


• 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 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.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.
Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755; [e-mail] [e-mail] [e-mail].
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.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232.
Virology Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892.
Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756.
Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037; [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.42 kDa 
• Atom Count: 7,532 
• Modeled Residue Count: 852 
• Deposited Residue Count: 902 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G4 antibody heavy chain	A [auth H], C [auth A]	233	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G4 antibody light chain	B [auth L], D [auth B]	218	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H], C [auth A]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/496

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.678	α = 90
b = 88.759	β = 90
c = 128.469	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Wang, N., Wrapp, D., McLellan, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI127521

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence
• Version 2.0: 2019-12-11
  Changes: Author supporting evidence, Polymer sequence
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary