7UGM

Crystal Structure of BG24-iGL CDR3mat Fab

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-03-25 Released: 2022-11-09 
  • Deposition Author(s): Dam, K.A., Barnes, C.O., Bjorkman, P.J.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design.

Dam, K.A., Barnes, C.O., Gristick, H.B., Schoofs, T., Gnanapragasam, P.N.P., Nussenzweig, M.C., Bjorkman, P.J.

(2022) Nat Commun 13: 6123-6123

  • DOI: https://doi.org/10.1038/s41467-022-33860-2
  • Primary Citation of Related Structures:  
    7UGM, 7UGN, 7UGO, 7UGP, 7UGQ

  • PubMed Abstract: 

    BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we report 4.1 Å and 3.4 Å single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures reveal critical Env contacts by BG24 iGL and identify antibody light chain structural features that impede Env recognition. In addition, biochemical data and cryo-EM structures of BG24 iGL variants bound to Envs with CD4bs glycans present provide insights into N-glycan accommodation, including structural modes of light chain adaptations in the presence of the N276 gp120 glycan. Together, these findings reveal Env regions critical for germline antibody recognition and potential sites to alter in immunogen design.

    • Organizational Affiliation: 

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BG24-iGL CDR3mat Fab heavy chainA [auth H]225Homo 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BG24-iGL CDR3mat Fab light chainB [auth L]209Homo 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: 1.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.254α = 90
b = 70.835β = 90
c = 134.846γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
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 StatesP01 AI100148
Bill & Melinda Gates FoundationUnited Statesgrant INV-002143

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description