5CGY

Fab fragment of Chikungunya virus neutralizing human monoclonal antibody 4J21

  • Classification: IMMUNE SYSTEM

  • Deposited: 2015-07-09 Released: 2015-11-11 
  • Deposition Author(s): Long, F., Crowe, J.E., Rossmann, M.G.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity.

Long, F.Fong, R.H.Austin, S.K.Chen, Z.Klose, T.Fokine, A.Liu, Y.Porta, J.Sapparapu, G.Akahata, W.Doranz, B.J.Crowe, J.E.Diamond, M.S.Rossmann, M.G.

(2015) Proc.Natl.Acad.Sci.USA 112: 13898-13903

  • DOI: 10.1073/pnas.1515558112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutral ...

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. Here, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain's β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. This finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes.


    Organizational Affiliation

    Department of Pediatrics, Vanderbilt University, Nashville, TN 37232; Departments of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37232; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232.,Department of Biological Sciences, Purdue University, West Lafayette, IN 47907; mr@purdue.edu.,Department of Biological Sciences, Purdue University, West Lafayette, IN 47907;,Integral Molecular, Inc., Philadelphia, PA 19104;,Departments of Medicine, Molecular Microbiology, Pathology, and Immunology, Washington University School of Medicine, St. Louis, MO 63110;,Department of Pediatrics, Vanderbilt University, Nashville, TN 37232;,VLP Therapeutics, LLC, Gaithersburg, MD 20878;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy Chain of Fab
H, C
228N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light Chain of Fab
L, D
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.224α = 90.00
b = 127.588β = 97.70
c = 83.912γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXrefinement
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 DiseasesUnited StatesRO1 AI095366
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesRO1 AI114816

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations