Evidence map›Paper›PMID 23708606›Full record

ArticleNature structural & molecular biology2013

Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120.

Leopold Kong, Jeong Hyun Lee, Katie J Doores, Charles D Murin, Jean-Philippe Julien, Ryan McBride, Yan Liu, Andre Marozsan, Albert Cupo, Per-Johan Klasse and 17 more

Abstract readVideo-Audio Media
In one paragraph

Article in Nature structural & molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 268 papers.

0numbers the graph read from it
0cells of the map it votes in
268citing papers in PubMed
–field-weighted citation impact
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

268 citing papers in PubMed.

  1. Trial
  2. Deletions in variable region 1 of the HIV envelope accelerate V3-glycan bNAb induction in SHIV-infected rhesus macaques.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
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  8. Review
  9. Article
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  13. ACS central science · 2025
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  19. Review
  20. Article

208 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

27 authors.

Leopold KongDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
Jeong Hyun Lee
Katie J Doores
Charles D Murin
Jean-Philippe Julien
Ryan McBride
Yan Liu
Andre Marozsan
Albert Cupo
Per-Johan Klasse
Simon Hoffenberg
Michael Caulfield
C Richter King
Yuanzi Hua
Khoa M Le
Reza Khayat
Marc C Deller
Thomas Clayton
Henry Tien
Ten Feizi
Rogier W Sanders
James C Paulson
John P Moore
Robyn L Stanfield
Dennis R Burton
Andrew B Ward
Ian A Wilson

Funding

Support Component D/Vaccine Discovery, Concept to ClinicUM1AI100663 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BAROUCH, DAN H. · 2012 to 2018
$131.5M
VirologyP30AI036214 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI David Mitchell Smith · 1994 to 2026
$78.4M
Structure Determination Core at SSRLU54GM094586 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI WILSON, IAN A · 2010 to 2014
$40.1M
Trimer Production and Immunogenicity TestingP01AI082362 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI MOORE, JOHN P · 2009 to 2014
$16.0M
TRD #3: An automated and streamlined pipeline for in-situ molecular microscopyP41GM103310 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI DE MARCO, ALEX, KIEFT, JEFFREY S · 2012 to 2021
$14.7M
WORKSHOPS AND TRAININGP41RR017573 · NCRR · SCRIPPS RESEARCH INSTITUTE, THE · PI CARRAGHER, BRIDGET OLIVIA · 2002 to 2011
$14.2M
NEUTRALIZATION OF PRIMARY HIV1 VIRUSESR37AI036082 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI MOORE, JOHN P · 1998 to 2017
$7.0M
HUMAN ANTIBODIES TO HIV-1 BY REPERTOIRE CLONINGR01AI033292 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BURTON, DENNIS R. · 1992 to 2013
$5.9M
X-ray structures of HIV-1 neutralizing sitesR01GM046192 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI WILSON, IAN A · 1991 to 2008
$3.7M
Structural Biology of HIV-1 Neutralizing Antibody Targets for Vaccine DesignR01AI084817 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI WILSON, IAN A · 2009 to 2013
$3.2M
Immunogenic sugar moieties of prostate cancersU01CA128416 · NCI · STANFORD UNIVERSITY · PI WANG, DENONG · 2007 to 2011
$2.3M
Howard Hughes Medical InstituteNCI NIH HHS U01 CA128416NCRR NIH HHS P41 RR017573NCRR NIH HHS RR017573NIAID NIH HHS P01 AI082362NIAID NIH HHS P01 AI82362NIAID NIH HHS P30 AI036214NIAID NIH HHS R01 AI033292NIAID NIH HHS R01 AI084817NIAID NIH HHS R01 AI33292NIAID NIH HHS R01 AI84817NIAID NIH HHS R37 AI036082NIAID NIH HHS R37 AI36082NIAID NIH HHS UM1 AI100663NIGMS NIH HHS P41 GM103310NIGMS NIH HHS R01 GM046192NIGMS NIH HHS U54 GM094586Wellcome Trust 099197Wellcome Trust WT093378MAWellcome Trust WT099197MA
6 · The paper itself

Abstract

A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb PGT 135 binds its Asn332 glycan-dependent epitope from its 3.1-Å crystal structure with gp120, CD4 and Fab 17b. PGT 135 interacts with glycans at Asn332, Asn392 and Asn386, using long CDR loops H1 and H3 to penetrate the glycan shield and access the gp120 protein surface. EM reveals that PGT 135 can accommodate the conformational and chemical diversity of gp120 glycans by altering its angle of engagement. Combined structural studies of PGT 135, PGT 128 and 2G12 show that this Asn332-dependent antigenic region is highly accessible and much more extensive than initially appreciated, which allows for multiple binding modes and varied angles of approach; thereby it represents a supersite of vulnerability for antibody neutralization.

Indexed as

1-DeoxynojirimycinAlkaloidsAmino Acid MotifsAmino Acid SequenceAntibodies, NeutralizingAntigen-Antibody ReactionsBinding Sites, AntibodyBiopolymersCarbohydrate SequenceCD4 AntigensCrystallography, X-Rayenv Gene Products, Human Immunodeficiency VirusEpitopesGlycosylationHEK293 CellsHIV Antibodies1-DeoxynojirimycinAlkaloidsAntibodies, NeutralizingBiopolymersCD4 Antigensenv Gene Products, Human Immunodeficiency VirusEpitopesgp120 protein, Human immunodeficiency virus 1gp140 envelope protein, Human immunodeficiency virus 1HIV AntibodiesHIV Envelope Protein gp120Immunoglobulin Fab FragmentskifunensinemiglustatPolysaccharides

Identifiers

PMID23708606
PMCPMC3823233

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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.