4O5L

Crystal structure of broadly neutralizing antibody F045-092


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus.

Lee, P.S.Ohshima, N.Stanfield, R.L.Yu, W.Iba, Y.Okuno, Y.Kurosawa, Y.Wilson, I.A.

(2014) Nat Commun 5: 3614-3614

  • DOI: 10.1038/ncomms4614
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Influenza viruses present a significant health challenge each year, as in the H3N2 epidemic of 2012-2013. Here we describe an antibody, F045-092, that possesses broadly neutralizing activity against the entire H3 subtype and accommodates the natural ...

    Influenza viruses present a significant health challenge each year, as in the H3N2 epidemic of 2012-2013. Here we describe an antibody, F045-092, that possesses broadly neutralizing activity against the entire H3 subtype and accommodates the natural variation and additional glycosylation in all strains tested from 1963 to 2011. Crystal structures of F045-092 in complex with HAs from 1975 and 2011 H3N2 viruses reveal the structural basis for its neutralization breadth through insertion of its 23-residue HCDR3 into the receptor-binding site that involves striking receptor mimicry. F045-092 extends its recognition to divergent subtypes, including H1, H2 and H13, using the enhanced avidity of its IgG to overcome lower-affinity Fab binding, as observed with other antibodies that target the receptor-binding site. This unprecedented level of antibody cross-reactivity against the H3 subtype can potentially inform on development of a pan-H3 vaccine or small-molecule therapeutics.


    Organizational Affiliation

    1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA [2] The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab F045-092 light chainL230Homo sapiensMutation(s): 0 
Gene Names: IGLC3
Find proteins for P0DOY3 (Homo sapiens)
Explore P0DOY3 
Go to UniProtKB:  P0DOY3
NIH Common Fund Data Resources
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab F045-092 heavy chainH240Homo sapiensMutation(s): 0 
Find proteins for A8K008 (Homo sapiens)
Explore A8K008 
Go to UniProtKB:  A8K008
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.515α = 90
b = 77.278β = 90
c = 81.451γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Database references
  • Version 1.2: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary