Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 1025.49 kDa 
• Atom Count: 28014 
• Modelled Residue Count: 3618 
• Deposited Residue Count: 9327 
• Unique protein chains: 3

5W9P

MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4

• DOI: 10.2210/pdb5W9P/pdb
• EMDataResource: EMD-8791

• Classification: VIRAL PROTEIN
• Organism(s): Middle East respiratory syndrome-related coronavirus, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2017-06-23 Released: 2017-08-16 
• Deposition Author(s): Pallesen, J., Ward, A.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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: 10.1073/pnas.1707304114
• Primary Citation of Related Structures:  
  5W9P, 5W9O, 5W9H, 5W9J, 5W9I, 5W9L, 5W9K, 5W9N, 5W9M, 5VYH, 5VZR


• 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 Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755; [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B [auth A], E [auth B], F [auth C], I [auth H], J [auth I], A [auth J]	1329	Middle East respiratory syndrome-related coronavirus	Mutation(s): 2
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N5Q8  Go to UniProtKB:  K9N5Q8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G4 VH	G [auth D], C [auth F], K	233	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
G4 VL	H [auth E], D [auth G], L	218	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-23 
• Released Date: 2017-08-16 
Deposition Author(s): Pallesen, J., Ward, A.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM113132
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI127521

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Data collection, Database references
• Version 1.3: 2017-11-08
  Changes: Derived calculations
• Version 1.4: 2018-07-18
  Changes: Data collection, Experimental preparation
• Version 1.5: 2020-01-01
  Changes: Author supporting evidence