4PY8

Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Alternative Recognition of the Conserved Stem Epitope in Influenza A Virus Hemagglutinin by a VH3-30-Encoded Heterosubtypic Antibody.

Wyrzucki, A.Dreyfus, C.Kohler, I.Steck, M.Wilson, I.A.Hangartner, L.

(2014) J.Virol. 88: 7083-7092

  • DOI: 10.1128/JVI.00178-14
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A human monoclonal heterosubtypic antibody, MAb 3.1, with its heavy chain encoded by VH3-30, was isolated using phage display with immobilized hemagglutinin (HA) from influenza virus A/Japan/305/1957(H2N2) as the target. Antibody 3.1 potently neutral ...

    A human monoclonal heterosubtypic antibody, MAb 3.1, with its heavy chain encoded by VH3-30, was isolated using phage display with immobilized hemagglutinin (HA) from influenza virus A/Japan/305/1957(H2N2) as the target. Antibody 3.1 potently neutralizes influenza viruses from the H1a clade (i.e., H1, H2, H5, H6) but has little neutralizing activity against the H1b clade. Its crystal structure in complex with HA from a pandemic H1N1 influenza virus, A/South Carolina/1/1918(H1N1), revealed that like other heterosubtypic anti-influenza virus antibodies, MAb 3.1 contacts a hydrophobic groove in the HA stem, primarily using its heavy chain. However, in contrast to the closely related monoclonal antibody (Mab) FI6 that relies heavily on HCDR3 for binding, MAb 3.1 utilizes residues from HCDR1, HCDR3, and framework region 3 (FR3). Interestingly, HCDR1 of MAb 3.1 adopts an α-helical conformation and engages in hydrophobic interactions with the HA very similar to those of the de novo in silico-designed and affinity-matured synthetic protein HB36.3. These findings improve our understanding of the molecular requirements for binding to the conserved epitope in the stem of the HA protein and, therefore, aid the development of more universal influenza vaccines targeting these epitopes.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA hangartner.lars@virology.uzh.ch wilson@scripps.edu.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland hangartner.lars@virology.uzh.ch wilson@scripps.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1 chain
A
331Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)Mutation(s): 0 
Gene Names: HA
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Go to UniProtKB:  Q9WFX3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2 chain
B
179Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)Mutation(s): 0 
Gene Names: HA
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Go to UniProtKB:  Q9WFX3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody 3.1 heavy chain
I
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
antibody 3.1 light chain
J
214N/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
MLI
Query on MLI

Download SDF File 
Download CCD File 
I, J
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 135.060α = 90.00
b = 135.060β = 90.00
c = 230.201γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
Blu-Icedata collection
PHASERphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-26 
  • Released Date: 2014-05-21 
  • Deposition Author(s): Dreyfus, C.

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-06-04
    Type: Database references