9BDI

Crystal structure of HIV-1 MPER scaffold in complex with antibody Fab Ab45.2

  • Classification: VIRAL PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Mus musculus
  • Mutation(s): No 

  • Deposited: 2024-04-11 Released: 2025-02-19 
  • Deposition Author(s): Lee, C.C.D., Wilson, I.A.
  • 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: 2.07 Å
  • R-Value Free: 
    0.283 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Affinity gaps among B cells in germinal centers drive the selection of MPER precursors.

Ray, R.Schiffner, T.Wang, X.Yan, Y.Rantalainen, K.Lee, C.D.Parikh, S.Reyes, R.A.Dale, G.A.Lin, Y.C.Pecetta, S.Giguere, S.Swanson, O.Kratochvil, S.Melzi, E.Phung, I.Madungwe, L.Kalyuzhniy, O.Warner, J.Weldon, S.R.Tingle, R.Lamperti, E.Kirsch, K.H.Phelps, N.Georgeson, E.Adachi, Y.Kubitz, M.Nair, U.Crotty, S.Wilson, I.A.Schief, W.R.Batista, F.D.

(2024) Nat Immunol 25: 1083-1096

  • DOI: https://doi.org/10.1038/s41590-024-01844-7
  • Primary Citation of Related Structures:  
    9BDH, 9BDI

  • PubMed Abstract: 

    Current prophylactic human immunodeficiency virus 1 (HIV-1) vaccine research aims to elicit broadly neutralizing antibodies (bnAbs). Membrane-proximal external region (MPER)-targeting bnAbs, such as 10E8, provide exceptionally broad neutralization, but some are autoreactive. Here, we generated humanized B cell antigen receptor knock-in mouse models to test whether a series of germline-targeting immunogens could drive MPER-specific precursors toward bnAbs. We found that recruitment of 10E8 precursors to germinal centers (GCs) required a minimum affinity for germline-targeting immunogens, but the GC residency of MPER precursors was brief due to displacement by higher-affinity endogenous B cell competitors. Higher-affinity germline-targeting immunogens extended the GC residency of MPER precursors, but robust long-term GC residency and maturation were only observed for MPER-HuGL18, an MPER precursor clonotype able to close the affinity gap with endogenous B cell competitors in the GC. Thus, germline-targeting immunogens could induce MPER-targeting antibodies, and B cell residency in the GC may be regulated by a precursor-competitor affinity gap.


  • Organizational Affiliation

    The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GT10.2 glycan KO
A, B
153Mus musculusMutation(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
Fab 45.2 Heavy ChainC,
E [auth H]
234Mus musculusMutation(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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 45.2 Light ChainD,
F [auth L]
214Mus musculusMutation(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: 2.07 Å
  • R-Value Free:  0.283 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.617α = 86.673
b = 46.638β = 86.76
c = 178.352γ = 77.044
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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 StatesAI144462
Bill & Melinda Gates FoundationUnited StatesINV-034657

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release