4GQ9

Chikungunya virus neutralizing antibody 9.8B Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.995 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.323 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.

Sun, S.Xiang, Y.Akahata, W.Holdaway, H.Pal, P.Zhang, X.Diamond, M.S.Nabel, G.J.Rossmann, M.G.

(2013) Elife 2: e00435-e00435

  • DOI: 10.7554/eLife.00435
  • Primary Citation of Related Structures:  3J2W, 3J2X, 3J2Y, 3J2Z, 3J30

  • PubMed Abstract: 
  • A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure wa ...

    A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment. DOI:http://dx.doi.org/10.7554/eLife.00435.001.


    Organizational Affiliation

    Department of Biological Sciences , Purdue University , West Lafayette , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chikungunya virus neutralizing antibody 9.8B Fab fragment light chain
L
212N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Chikungunya virus neutralizing antibody 9.8B Fab fragment heavy chain
H
218N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.995 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.323 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.859α = 90.00
b = 57.726β = 97.51
c = 118.108γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-22 
  • Released Date: 2013-07-10 
  • Deposition Author(s): Sun, S, Rossmann, M.G.

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release