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 8VVB | pdb_00008vvb

Influenza antibody L5A7 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Anti-idiotype isolation of a broad and potent influenza A virus-neutralizing human antibody.

Olia, A.S., Prabhakaran, M., Harris, D.R., Cheung, C.S., Gillespie, R.A., Gorman, J., Hoover, A., Morano, N.C., Ourahmane, A., Srikanth, A., Wang, S., Wu, W., Zhou, T., Andrews, S.F., Kanekiyo, M., Shapiro, L., McDermott, A.B., Kwong, P.D.

(2024) Front Immunol 15: 1399960-1399960

  • DOI: https://doi.org/10.3389/fimmu.2024.1399960
  • Primary Citation Related Structures: 
    8VUE, 8VUZ, 8VVB

  • PubMed Abstract: 

    The VH6-1 class of antibodies includes some of the broadest and most potent antibodies that neutralize influenza A virus. Here, we elicit and isolate anti-idiotype antibodies against germline versions of VH6-1 antibodies, use these to sort human leukocytes, and isolate a new VH6-1-class member, antibody L5A7, which potently neutralized diverse group 1 and group 2 influenza A strains. While its heavy chain derived from the canonical IGHV6-1 heavy chain gene used by the class, L5A7 utilized a light chain gene, IGKV1-9, which had not been previously observed in other VH6-1-class antibodies. The cryo-EM structure of L5A7 in complex with Indonesia 2005 hemagglutinin revealed a nearly identical binding mode to other VH6-1-class members. The structure of L5A7 bound to the isolating anti-idiotype antibody, 28H6E11, revealed a shared surface for binding anti-idiotype and hemagglutinin that included two critical L5A7 regions: an FG motif in the third heavy chain-complementary determining region (CDR H3) and the CDR L1 loop. Surprisingly, the chemistries of L5A7 interactions with hemagglutinin and with anti-idiotype were substantially different. Overall, we demonstrate anti-idiotype-based isolation of a broad and potent influenza A virus-neutralizing antibody, revealing that anti-idiotypic selection of antibodies can involve features other than chemical mimicry of the target antigen.


  • Organizational Affiliation: 
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.

Macromolecule Content 

  • Total Structure Weight: 94.72 kDa 
  • Atom Count: 7,722 
  • Modeled Residue Count: 862 
  • Deposited Residue Count: 880 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L5A7 Heavy Chain
A, C
230Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
L5A7 Light Chain
B, D
210Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.76α = 90
b = 109.19β = 90
c = 140.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary