Evidence map›Paper›PMID 35136084›Full record

ArticleNature communications2022

Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer.

Zhi Yang, Kim-Marie A Dam, Michael D Bridges, Magnus A G Hoffmann, Andrew T DeLaitsch, Harry B Gristick, Amelia Escolano, Rajeev Gautam, Malcolm A Martin, Michel C Nussenzweig and 2 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.

0numbers the graph read from it
0cells of the map it votes in
27citing papers in PubMed
2.7field-weighted citation impact, top 8% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

27 citing papers in PubMed, 38 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 5 institutions in 1 country.

Zhi YangDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Kim-Marie A DamDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0002-1416-4757
Michael D BridgesJules Stein Eye Institute, University of California, Los Angeles, CA, USA.
Magnus A G HoffmannDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0003-4923-9568
Andrew T DeLaitschDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0002-3458-3449
Harry B GristickDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Amelia EscolanoLaboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
Rajeev GautamLaboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Malcolm A MartinLaboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Michel C NussenzweigLaboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
Wayne L HubbellJules Stein Eye Institute, University of California, Los Angeles, CA, USA.
Pamela J BjorkmanDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. bjorkman@caltech.edu.ORCID http://orcid.org/0000-0002-2277-3990
California Institute of Technology · USNational Institutes of Health · USUniversity of California, Los Angeles · USHoward Hughes Medical Institute · USRockefeller University · US

Funding

Identification of neutralizing epitopes on SARS-CoV-2 spike for design of vaccines and small-molecule antiviralsUM1AI144462 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BURTON, DENNIS R. · 2019 to 2025
$201.6M
Virus & Reservoirs CoreP30AI045008 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI DAVID S METZGER · 1999 to 2026
$78.6M
Stuctural basis of bNab activityP01AI100148 · NIAID · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI Pamela J Bjorkman · 2013 to 2026
$43.3M
X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
The Biology of HIV InfectionsZIAAI001213 · NIAID · NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES · PI MARTIN, MALCOLM · 2016 to 2025
$23.7M
Vision Research Core at UCLAP30EY000331 · NEI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Xian-Jie Yang · 1985 to 2026
$16.8M
Virus TransmissionP50AI150464 · NIAID · UNIVERSITY OF UTAH · PI SUNDQUIST, WESLEY I. · 2019 to 2021
$14.9M
Recombinant HIV-1 Env glycoprotein immunogens and antibodies production and structural characterizationP01AI138212 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MCGUIRE, ANDREW · 2019 to 2023
$9.2M
Design of vaccination strategies to elicit broadly neutralizing antibodies against HIV-1R00AI140770 · NIAID · WISTAR INSTITUTE · PI ESCOLANO, AMELIA · 2021 to 2022
$498k
Design of vaccination strategies to elicit broadly neutralizing antibodies against HIV-1K99AI140770 · NIAID · ROCKEFELLER UNIVERSITY · PI ESCOLANO, AMELIA · 2019 to 2020
$262k
Gates Foundation INV-002143Howard Hughes Medical InstituteNEI NIH HHS P30 EY000331NIAID NIH HHS K99 AI140770NIAID NIH HHS P01 AI100148NIAID NIH HHS P01 AI138212NIAID NIH HHS P30 AI045008NIAID NIH HHS P50 AI150464NIAID NIH HHS R00 AI140770NIAID NIH HHS UM1 AI144462NIGMS NIH HHS P41 GM103393
6 · The paper itself

Abstract

Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an 'occluded-open' conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts.

Indexed as

AnimalsAntibodies, NeutralizingBinding SitesCD4 AntigensCryoelectron MicroscopyCrystallography, X-RayDrug Designenv Gene Products, Human Immunodeficiency VirusHIV-1HIV AntibodiesHIV InfectionsHumansMacacaMolecular Docking SimulationProtein BindingProtein DomainsAntibodies, NeutralizingCD4 Antigensenv Gene Products, Human Immunodeficiency VirusHIV Antibodies

Identifiers

PMID35136084
PMCPMC8826976
OpenAlexW4221060334

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.