3GBM

Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibody recognition of a highly conserved influenza virus epitope.

Ekiert, D.C.Bhabha, G.Elsliger, M.A.Friesen, R.H.Jongeneelen, M.Throsby, M.Goudsmit, J.Wilson, I.A.

(2009) Science 324: 246-251

  • DOI: 10.1126/science.1171491
  • Primary Citation of Related Structures:  3GBN

  • PubMed Abstract: 
  • Influenza virus presents an important and persistent threat to public health worldwide, and current vaccines provide immunity to viral isolates similar to the vaccine strain. High-affinity antibodies against a conserved epitope could provide immunity ...

    Influenza virus presents an important and persistent threat to public health worldwide, and current vaccines provide immunity to viral isolates similar to the vaccine strain. High-affinity antibodies against a conserved epitope could provide immunity to the diverse influenza subtypes and protection against future pandemic viruses. Cocrystal structures were determined at 2.2 and 2.7 angstrom resolutions for broadly neutralizing human antibody CR6261 Fab in complexes with the major surface antigen (hemagglutinin, HA) from viruses responsible for the 1918 H1N1 influenza pandemic and a recent lethal case of H5N1 avian influenza. In contrast to other structurally characterized influenza antibodies, CR6261 recognizes a highly conserved helical region in the membrane-proximal stem of HA1 and HA2. The antibody neutralizes the virus by blocking conformational rearrangements associated with membrane fusion. The CR6261 epitope identified here should accelerate the design and implementation of improved vaccines that can elicit CR6261-like antibodies, as well as antibody-based therapies for the treatment of influenza.


    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A, C
334Influenza A virus (A/Viet Nam/1203/2004(H5N1))Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus (A/Viet Nam/1203/2004(H5N1)))
Go to UniProtKB:  Q6DQ33
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B, D
177Influenza A virus (A/Viet Nam/1203/2004(H5N1))Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus (A/Viet Nam/1203/2004(H5N1)))
Go to UniProtKB:  Q6DQ33
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody (Fab)
H, I
226N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
antibody (Fab)
L, M
221N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 202.761α = 90.00
b = 202.761β = 90.00
c = 202.761γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
PHASERphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance