4ZPT | pdb_00004zpt

Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 1)

• PDB DOI: https://doi.org/10.2210/pdb4ZPT/pdb

• Classification: Viral protein/Immune system
• Organism(s): Mus musculus, Betacoronavirus England 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-05-08 Released: 2015-10-21 
• Deposition Author(s): Joyce, M.G., Mascola, J.R., Graham, B.S., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Evaluation of candidate vaccine approaches for MERS-CoV

Joyce, M.G.

(2015) Nat Commun 6: 7712

• PubMed: 26218507 
• DOI: https://doi.org/10.1038/ncomms8712
• Primary Citation Related Structures: 
  4ZPT, 4ZPV, 4ZPW


• PubMed Abstract: 
  

  The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) as a cause of severe respiratory disease highlights the need for effective approaches to CoV vaccine development. Efforts focused solely on the receptor-binding domain (RBD) of the viral Spike (S) glycoprotein may not optimize neutralizing antibody (NAb) responses. Here we show that immunogens based on full-length S DNA and S1 subunit protein elicit robust serum-neutralizing activity against several MERS-CoV strains in mice and non-human primates. Serological analysis and isolation of murine monoclonal antibodies revealed that immunization elicits NAbs to RBD and, non-RBD portions of S1 and S2 subunit. Multiple neutralization mechanisms were demonstrated by solving the atomic structure of a NAb-RBD complex, through sequencing of neutralization escape viruses and by constructing MERS-CoV S variants for serological assays. Immunization of rhesus macaques confers protection against MERS-CoV-induced radiographic pneumonia, as assessed using computerized tomography, supporting this strategy as a promising approach for MERS-CoV vaccine development.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
1] Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA [2] U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA [3] Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland 20817, USA.
1] Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Sanofi-Aventis, 270 Albany Street, Cambridge, Massachusetts 02139, USA.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.
Emerging Respiratory Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland,21702, USA.
1] Center for Infectious Disease Imaging, Department of Radiology and Imaging Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Center for Research in Computer Vision (CRCV), University of Central Florida, Orlando, Florida 32816, USA.
Center for Infectious Disease Imaging, Department of Radiology and Imaging Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA.
1] Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA [2] Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 140.09 kDa 
• Atom Count: 10,054 
• Modeled Residue Count: 1,267 
• Deposited Residue Count: 1,276 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D12 Fab Heavy chain	A, D [auth H]	216	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D12 Fab Light chain	B, F [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth R], E [auth S]	208	Betacoronavirus England 1	Mutation(s): 0  Gene Names: S, 3
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N5Q8  Go to UniProtKB:  K9N5Q8
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth R], H [auth S]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.452	α = 90
b = 128.79	β = 90
c = 170.871	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Joyce, M.G., Mascola, J.R., Graham, B.S., Kwong, P.D.

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary