6WF1

Crystal Structure of Broadly Neutralizing Antibody 3I14 Bound to the Influenza A H10 Hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.266 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Unique structural solution from a V H 3-30 antibody targeting the hemagglutinin stem of influenza A viruses.

Harshbarger, W.D.Deming, D.Lockbaum, G.J.Attatippaholkun, N.Kamkaew, M.Hou, S.Somasundaran, M.Wang, J.P.Finberg, R.W.Zhu, Q.K.Schiffer, C.A.Marasco, W.A.

(2021) Nat Commun 12: 559-559

  • DOI: https://doi.org/10.1038/s41467-020-20879-6
  • Primary Citation of Related Structures:  
    6WEX, 6WEZ, 6WF0, 6WF1

  • PubMed Abstract: 

    Broadly neutralizing antibodies (bnAbs) targeting conserved influenza A virus (IAV) hemagglutinin (HA) epitopes can provide valuable information for accelerating universal vaccine designs. Here, we report structural details for heterosubtypic recognition of HA from circulating and emerging IAVs by the human antibody 3I14. Somatic hypermutations play a critical role in shaping the HCDR3, which alone and uniquely among V H 3-30 derived antibodies, forms contacts with five sub-pockets within the HA-stem hydrophobic groove. 3I14 light-chain interactions are also key for binding HA and contribute a large buried surface area spanning two HA protomers. Comparison of 3I14 to bnAbs from several defined classes provide insights to the bias selection of V H 3-30 antibodies and reveals that 3I14 represents a novel structural solution within the V H 3-30 repertoire. The structures reported here improve our understanding of cross-group heterosubtypic binding activity, providing the basis for advancing immunogen designs aimed at eliciting a broadly protective response to IAV.


  • Organizational Affiliation

    Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin323Influenza A virusMutation(s): 0 
UniProt
Find proteins for A0A059T4A1 (Influenza A virus)
Explore A0A059T4A1 
Go to UniProtKB:  A0A059T4A1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059T4A1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain220Influenza A virusMutation(s): 0 
UniProt
Find proteins for A0A059T4A1 (Influenza A virus)
Explore A0A059T4A1 
Go to UniProtKB:  A0A059T4A1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059T4A1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
heavy chainC [auth H]231Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
light chainD [auth L]213Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.266 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.021α = 90
b = 127.021β = 90
c = 158.37γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

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 StatesR01AI121285
Department of Defense (DOD, United States)United StatesW81XWH-15-1-0317

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary