3IYW

West Nile virus in complex with Fab fragments of MAb CR4354 (fitted coordinates of envelope proteins and Fab fragments of one icosahedral ASU)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Neutralization of West Nile virus by cross-linking of its surface proteins with Fab fragments of the human monoclonal antibody CR4354.

Kaufmann, B.Vogt, M.R.Goudsmit, J.Holdaway, H.A.Aksyuk, A.A.Chipman, P.R.Kuhn, R.J.Diamond, M.S.Rossmann, M.G.

(2010) Proc.Natl.Acad.Sci.USA 107: 18950-18955

  • DOI: 10.1073/pnas.1011036107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many flaviviruses are significant human pathogens, with the humoral immune response playing an essential role in restricting infection and disease. CR4354, a human monoclonal antibody isolated from a patient, neutralizes West Nile virus (WNV) infecti ...

    Many flaviviruses are significant human pathogens, with the humoral immune response playing an essential role in restricting infection and disease. CR4354, a human monoclonal antibody isolated from a patient, neutralizes West Nile virus (WNV) infection at a postattachment stage in the viral life-cycle. Here, we determined the structure of WNV complexed with Fab fragments of CR4354 using cryoelectron microscopy. The outer glycoprotein shell of a mature WNV particle is formed by 30 rafts of three homodimers of the viral surface protein E. CR4354 binds to a discontinuous epitope formed by protein segments from two neighboring E molecules, but does not cause any detectable structural disturbance on the viral surface. The epitope occurs at two independent positions within an icosahedral asymmetric unit, resulting in 120 binding sites on the viral surface. The cross-linking of the six E monomers within one raft by four CR4354 Fab fragments suggests that the antibody neutralizes WNV by blocking the pH-induced rearrangement of the E protein required for virus fusion with the endosomal membrane.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
A, B, C
403West Nile virus (strain NY-99)Mutation(s): 0 
Gene Names: GP1
Find proteins for Q9Q6P4 (West Nile virus (strain NY-99))
Go to UniProtKB:  Q9Q6P4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CR4354 Fab fragment X1, heavy chain H
H, K
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CR4354 Fab fragment X1, light chain L
L, M
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, B, C
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
A, B, C
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H, K
L-PEPTIDE LINKINGC5 H7 N O3GLU
NDG
Query on NDG
A, B, C
D-SACCHARIDEC8 H15 N O6

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FUL
Query on FUL
A, B, C
L-SACCHARIDEC6 H12 O5

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-07-18
    Type: Data collection