7UGM | pdb_00007ugm

Crystal Structure of BG24-iGL CDR3mat Fab

• PDB DOI: https://doi.org/10.2210/pdb7UGM/pdb

• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.208 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 

Starting Model: experimental

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

• PubMed: 36253376 
• DOI: https://doi.org/10.1038/s41467-022-33860-2
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Department of Biology, Stanford University, Stanford, CA, USA.
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
Laboratory of Experimental Immunology, Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany.
German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany.
GlaxoSmithKline Vaccines, 1330, Rixensart, Belgium.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.2 kDa 
• Atom Count: 3,636 
• Modeled Residue Count: 426 
• Deposited Residue Count: 434 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BG24-iGL CDR3mat Fab heavy chain	A [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG24-iGL CDR3mat Fab light chain	B [auth L]	209	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.208 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.254	α = 90
b = 70.835	β = 90
c = 134.846	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Dam, K.A., Barnes, C.O., Bjorkman, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI100148
Bill & Melinda Gates Foundation	United States	grant INV-002143

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary