7L85

Designed tetrahedral nanoparticle T33-31 presenting BG505 SOSIP trimers


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM.

Antanasijevic, A.Sewall, L.M.Cottrell, C.A.Carnathan, D.G.Jimenez, L.E.Ngo, J.T.Silverman, J.B.Groschel, B.Georgeson, E.Bhiman, J.Bastidas, R.LaBranche, C.Allen, J.D.Copps, J.Perrett, H.R.Rantalainen, K.Cannac, F.Yang, Y.R.de la Pena, A.T.Rocha, R.F.Berndsen, Z.T.Baker, D.King, N.P.Sanders, R.W.Moore, J.P.Crotty, S.Crispin, M.Montefiori, D.C.Burton, D.R.Schief, W.R.Silvestri, G.Ward, A.B.

(2021) Nat Commun 12: 4817-4817

  • DOI: https://doi.org/10.1038/s41467-021-25087-4
  • Primary Citation of Related Structures:  
    7L7T, 7L7U, 7L85, 7L86, 7L87, 7L88, 7L89, 7L8A, 7L8B, 7L8C, 7L8D, 7L8E, 7L8F, 7L8G, 7L8S, 7L8T, 7L8U, 7L8W, 7L8X, 7L8Y, 7L8Z, 7L90

  • PubMed Abstract: 

    Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic.


  • Organizational Affiliation

    Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BG505 SOSIP-T33-31B125Human immunodeficiency virus 1Mutation(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
BG505 SOSIP-T33-31A106Human immunodeficiency virus 1Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTCoot
MODEL REFINEMENTRosettaEM

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
International AIDS Vaccine InitiativeUnited StatesOPP1196345

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection, Refinement description