Aleksandar Antanasijevic / Leigh M Sewall / Christopher A Cottrell / Diane G Carnathan / Luis E Jimenez / Julia T Ngo / Jennifer B Silverman / Bettina Groschel / Erik Georgeson / Jinal Bhiman / Raiza Bastidas / Celia LaBranche / Joel D Allen / Jeffrey Copps / Hailee R Perrett / Kimmo Rantalainen / Fabien Cannac / Yuhe R Yang / Alba Torrents de la Peña / Rebeca Froes Rocha / Zachary T Berndsen / David Baker / Neil P King / Rogier W Sanders / John P Moore / Shane Crotty / Max Crispin / David C Montefiori / Dennis R Burton / William R Schief / Guido Silvestri / Andrew B Ward /
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 ...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.
EMDB-23175: nsEM maps of BG505 SOSIP MD39 in complex with the polyclonal Fab samples from Group 1 of immunized rhesus macaques (Animal IDs: Rh.32034, Rh.32113, Rh.33104, Rh.33395, Rh.34909, Rh.34943) Method: EM (single particle) / Resolution: 20.0 Å
EMDB-23176: nsEM maps of BG505 SOSIP.v5.2 in complex with the polyclonal Fab samples from Group 2 of immunized rhesus macaques (Animal IDs: Rh.33182, Rh.33203, Rh.33311, Rh.34686, Rh.CD99, Rh.CG41) Method: EM (single particle) / Resolution: 20.0 Å
EMDB-23177: nsEM maps of BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab samples from Group 3 of immunized rhesus macaques (Wk8 time point; Animal IDs: Rh.33172, Rh.34919, Rh.34167, Rh.33065, Rh.33176, Rh.34725) Method: EM (single particle) / Resolution: 20.0 Å
EMDB-23178: nsEM maps of BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab samples from Group 3 of immunized rhesus macaques (Wk10 time point; Animal IDs: Rh.33172, Rh.34919, Rh.34167, Rh.33065, Rh.33176, Rh.34725) Method: EM (single particle) / Resolution: 20.0 Å
EMDB-23179: nsEM maps of BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab samples from Group 3 of immunized rhesus macaques (Wk26 time point; Animal IDs: Rh.33172, Rh.34919, Rh.34167, Rh.33065, Rh.34725) Method: EM (single particle) / Resolution: 20.0 Å
EMDB-23180: nsEM maps of BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab samples from Group 3 of immunized rhesus macaques (Wk38 time point; Animal IDs: Rh.33172, Rh.34919, Rh.34167, Rh.33065, Rh.34725) Method: EM (single particle) / Resolution: 20.0 Å
EMDB-23181: nsEM map of BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab sample from animal Rh.33172 (Wk26 time point) Method: EM (single particle) / Resolution: 19.7 Å
EMDB-23182: nsEM map of BG505 SOSIP.v3 in complex with the polyclonal Fab sample from animal Rh.33172 (Wk26 time point) Method: EM (single particle) / Resolution: 19.7 Å
EMDB-23183: nsEM map of BG505 SOSIP.v3 in complex with the polyclonal Fab sample from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 19.7 Å
EMDB-23184: nsEM map of BG505 SOSIP.v5.2 in complex with the polyclonal Fab sample from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 18.7 Å
EMDB-23185: BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31A Method: EM (single particle) / Resolution: 15.6 Å
EMDB-23186: BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B Method: EM (single particle) / Resolution: 15.6 Å
EMDB-23218, PDB-7l7t: BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component A) Method: EM (single particle) / Resolution: 3.7 Å
EMDB-23219, PDB-7l7u: BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) Method: EM (single particle) / Resolution: 3.8 Å
EMDB-23223, PDB-7l86: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-1 from animal Rh.32034 (Wk26 time point) Method: EM (single particle) / Resolution: 3.4 Å
EMDB-23224, PDB-7l87: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-2 from animal Rh.32034 (Wk26 time point) Method: EM (single particle) / Resolution: 3.6 Å
EMDB-23225, PDB-7l88: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point) Method: EM (single particle) / Resolution: 3.6 Å
EMDB-23226, PDB-7l89: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-4 from animal Rh.32034 (Wk26 time point) Method: EM (single particle) / Resolution: 3.8 Å
EMDB-23227, PDB-7l8a: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-1 from animal Rh.33104 (Wk26 time point) Method: EM (single particle) / Resolution: 3.3 Å
EMDB-23228, PDB-7l8b: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-2 from animal Rh.33104 (Wk26 time point) Method: EM (single particle) / Resolution: 3.7 Å
EMDB-23229, PDB-7l8c: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point) Method: EM (single particle) / Resolution: 3.4 Å
EMDB-23230, PDB-7l8d: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-4 from animal Rh.33104 (Wk26 time point) Method: EM (single particle) / Resolution: 4.6 Å
EMDB-23231, PDB-7l8e: BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-1 from animal Rh.33172 (Wk38 time point) Method: EM (single particle) / Resolution: 4.2 Å
EMDB-23232, PDB-7l8f: BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-2 from animal Rh.33172 (Wk38 time point) Method: EM (single particle) / Resolution: 3.66 Å
EMDB-23233, PDB-7l8g: BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-3 from animal Rh.33172 (Wk38 time point) Method: EM (single particle) / Resolution: 4.3 Å
EMDB-23234: BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-5 from animal Rh.33172 (Wk38 time point) Method: EM (single particle) / Resolution: 4.5 Å
EMDB-23235, PDB-7l8s: BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-4 from animal Rh.33172 (Wk38 time point) Method: EM (single particle) / Resolution: 4.3 Å
EMDB-23236, PDB-7l8t: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-1 from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 3.7 Å
EMDB-23237, PDB-7l8u: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 4.5 Å
EMDB-23238, PDB-7l8w: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-3 from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 4.1 Å
EMDB-23239, PDB-7l8x: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-4 from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 3.0 Å
EMDB-23240, PDB-7l8y: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-5 from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 4.2 Å
EMDB-23241: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-6 from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 6.6 Å
EMDB-23242, PDB-7l8z: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-7 from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 3.8 Å
EMDB-23243, PDB-7l90: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 from animal Rh.33311 (Wk26 time point) Method: EM (single particle) / Resolution: 4.5 Å
VIRAL PROTEIN / HIV / vaccine design / protein design / nanoparticles / BG505 / DE NOVO PROTEIN / VIRAL PROTEIN/Immune System / Polyclonal antibodies / EMPEM / VIRAL PROTEIN-Immune System complex
+
About Yorodumi Papers
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Movie
Controller
Structure viewers
About Yorodumi Papers
Authors
External links
Keywords
human immunodeficiency virus 1
macaca mulatta (Rhesus monkey)