5DO2

Complex structure of MERS-RBD bound with 4C2 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein.

Li, Y.Wan, Y.Liu, P.Zhao, J.Lu, G.Qi, J.Wang, Q.Lu, X.Wu, Y.Liu, W.Zhang, B.Yuen, K.Y.Perlman, S.Gao, G.F.Yan, J.

(2015) Cell Res 25: 1237-1249

  • DOI: https://doi.org/10.1038/cr.2015.113
  • Primary Citation of Related Structures:  
    5DO2

  • PubMed Abstract: 

    The newly-emerging Middle East respiratory syndrome coronavirus (MERS-CoV) can cause severe and fatal acute respiratory disease in humans. Despite global efforts, the potential for an associated pandemic in the future cannot be excluded. The development of effective counter-measures is urgent. MERS-CoV-specific anti-viral drugs or vaccines are not yet available. Using the spike receptor-binding domain of MERS-CoV (MERS-RBD) to immunize mice, we identified two neutralizing monoclonal antibodies (mAbs) 4C2 and 2E6. Both mAbs potently bind to MERS-RBD and block virus entry in vitro with high efficacy. We further investigated their mechanisms of neutralization by crystallizing the complex between the Fab fragments and the RBD, and solved the structure of the 4C2 Fab/MERS-RBD complex. The structure showed that 4C2 recognizes an epitope that partially overlaps the receptor-binding footprint in MERS-RBD, thereby interfering with the virus/receptor interactions by both steric hindrance and interface-residue competition. 2E6 also blocks receptor binding, and competes with 4C2 for binding to MERS-RBD. Based on the structure, we further humanized 4C2 by preserving only the paratope residues and substituting the remaining amino acids with the counterparts from human immunoglobulins. The humanized 4C2 (4C2h) antibody sustained similar neutralizing activity and biochemical characteristics to the parental mouse antibody. Finally, we showed that 4C2h can significantly abate the virus titers in lungs of Ad5-hCD26-transduced mice infected with MERS-CoV, therefore representing a promising agent for prophylaxis and therapy in clinical settings.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S proteinA,
D [auth B]
251Middle East respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for W5ZZM0 (Middle East respiratory syndrome-related coronavirus)
Explore W5ZZM0 
Go to UniProtKB:  W5ZZM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5ZZM0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
4C2 heavy chainB [auth H],
E [auth C]
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
4C2 light chainC [auth L],
F [auth D]
214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.083α = 90
b = 110.401β = 90
c = 172.981γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-06
    Changes: Structure summary