5WKO

Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1) influenza virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Antibody 27F3 Broadly Targets Influenza A Group 1 and 2 Hemagglutinins through a Further Variation in VH1-69 Antibody Orientation on the HA Stem.

Lang, S.Xie, J.Zhu, X.Wu, N.C.Lerner, R.A.Wilson, I.A.

(2017) Cell Rep 20: 2935-2943

  • DOI: https://doi.org/10.1016/j.celrep.2017.08.084
  • Primary Citation of Related Structures:  
    5WKO

  • PubMed Abstract: 

    Antibodies that target both group 1 and group 2 influenza A viruses are valuable for therapeutic and vaccine development, but only a few have been reported to date. Here, we describe a new V H 1-69 antibody 27F3 that broadly recognizes heterosubtypic hemagglutinins (HAs) from both group 1 and group 2 influenza A viruses. Structural characterization of 27F3 Fab with A/California/04/2009 (H1N1) hemagglutinin illustrates that 27F3 shares the key binding features observed in other V H 1-69 antibodies to the HA stem. Compared to other V H 1-69 antibodies, the 27F3 V H domain interacts with the HA stem in a distinct orientation, which alters its epitope and may have influenced its breadth. The diverse rotations of V H 1-69 antibodies on the HA stem epitope highlight the different ways that this antibody family can evolve to broadly neutralize influenza A viruses. These results have important implications for understanding how to elicit broad antibody responses against influenza virus.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 27F3 heavy chain
A, C, E, G, I
A, C, E, G, I, K
225Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6N089 (Homo sapiens)
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Go to UniProtKB:  Q6N089
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UniProt GroupQ6N089
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 27F3 light chain
B, D, F, H, J
B, D, F, H, J, L
213Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q9UL78 (Homo sapiens)
Explore Q9UL78 
Go to UniProtKB:  Q9UL78
Find proteins for Q6P5S8 (Homo sapiens)
Explore Q6P5S8 
Go to UniProtKB:  Q6P5S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ6P5S8Q9UL78
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
M, N, O, S, T
M, N, O, S, T, U
331Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
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Go to UniProtKB:  C3W5S1
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UniProt GroupC3W5S1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
P, Q, R, V, W
P, Q, R, V, W, X
177Influenza A virus (A/Uganda/MUWRP-176/2010(H1N1))Mutation(s): 1 
Gene Names: HA
UniProt
Find proteins for C5MVT7 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C5MVT7 
Go to UniProtKB:  C5MVT7
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UniProt GroupC5MVT7
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.58α = 90
b = 191.486β = 90
c = 391.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI117675

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-11
    Changes: Advisory, Author supporting evidence, Derived calculations
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description