Evidence map›Paper›PMID 23708607›Full record

ArticleNature structural & molecular biology2013

Structural basis for diverse N-glycan recognition by HIV-1-neutralizing V1-V2-directed antibody PG16.

Marie Pancera, Syed Shahzad-Ul-Hussan, Nicole A Doria-Rose, Jason S McLellan, Robert T Bailer, Kaifan Dai, Sandra Loesgen, Mark K Louder, Ryan P Staupe, Yongping Yang and 15 more

Open access · greenAbstract read
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 217 papers.

0numbers the graph read from it
0cells of the map it votes in
217citing papers in PubMed
15.0field-weighted citation impact, top 1% 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

217 citing papers in PubMed, 275 citations in OpenAlex.

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors at 6 institutions in 1 country.

Marie PanceraVaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA.
Syed Shahzad-Ul-Hussan
Nicole A Doria-Rose
Jason S McLellan
Robert T Bailer
Kaifan Dai
Sandra Loesgen
Mark K Louder
Ryan P Staupe
Yongping Yang
Baoshan Zhang
Robert Parks
Joshua Eudailey
Krissey E Lloyd
Julie Blinn
S Munir Alam
Barton F Haynes
Mohammed N Amin
Lai-Xi Wang
Dennis R Burton
Wayne C Koff
Gary J Nabel
John R Mascola
Carole A Bewley
Peter D Kwong
National Institutes of Health · USDuke Medical Center · USNational Institute of Allergy and Infectious Diseases · USUniversity of Maryland, Baltimore · USInternational AIDS Vaccine Initiative · USScripps Research Institute · US

Funding

Viral Sequencing CoreU19AI067854 · NIAID · DUKE UNIVERSITY · PI HARRISON, STEPHEN COPLAN · 2006 to 2011
$290.5M
Virus biology scientific research support componentUM1AI100645 · NIAID · DUKE UNIVERSITY · PI MCMICHAEL, ANDREW JAMES · 2012 to 2018
$204.7M
Virology Research Program (Program 4)P30CA016086 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Deborah F. Tate · 1985 to 2026
$201.5M
Neutralization Mechanisms Of Anti-HIV-1 Monoclonal AntibodiesZIAAI005022 · NIAID · NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES · PI ZHOU, TONGQING · 2009 to 2025
$24.6M
ZINC DEFICIENCY &PROTEIN EXPRESSION IN RAT OLFACTORY BULBSP41RR018502 · NCRR · UNIVERSITY OF GEORGIA (UGA) · PI AZADI, PARASTOO · 2003 to 2011
$13.1M
Inhibitors and Probes of HIV-1 Cell FusionZIADK032103 · NIDDK · NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES · PI BEWLEY, CAROLE · 2009 to 2025
$12.5M
Synthetic Variable Domain Glycopeptides for Neutralizing Epitope CharacterizationR21AI101035 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI PAUZA, C. DAVID · 2012 to 2013
$411k
Intramural NIH HHS ZIA DK032103NCI NIH HHS P30 CA016086NCRR NIH HHS P41 RR018502NCRR NIH HHS P41 RR018502-01NIAID NIH HHS 1R21 AI101035NIAID NIH HHS AI 5U19 AI 067854-06NIAID NIH HHS R21 AI101035NIAID NIH HHS U19 AI067854NIAID NIH HHS UM1 AI100645
6 · The paper itself

Abstract

HIV-1 uses a diverse N-linked-glycan shield to evade recognition by antibody. Select human antibodies, such as the clonally related PG9 and PG16, recognize glycopeptide epitopes in the HIV-1 V1-V2 region and penetrate this shield, but their ability to accommodate diverse glycans is unclear. Here we report the structure of antibody PG16 bound to a scaffolded V1-V2, showing an epitope comprising both high mannose-type and complex-type N-linked glycans. We combined structure, NMR and mutagenesis analyses to characterize glycan recognition by PG9 and PG16. Three PG16-specific residues, arginine, serine and histidine (RSH), were critical for binding sialic acid on complex-type glycans, and introduction of these residues into PG9 produced a chimeric antibody with enhanced HIV-1 neutralization. Although HIV-1-glycan diversity facilitates evasion, antibody somatic diversity can overcome this and can provide clues to guide the design of modified antibodies with enhanced neutralization.

Indexed as

Amino Acid MotifsAmino Acid SequenceAntibodies, NeutralizingAntibody SpecificityAntigen-Antibody ReactionsBinding Sites, AntibodyCarbohydrate ConformationCarbohydrate SequenceCrystallography, X-RayEpitopesGlycosylationHEK293 CellsHIV AntibodiesHIV Envelope Protein gp120HumansImmunoglobulin Fab FragmentsAntibodies, NeutralizingEpitopesgp120 protein, Human immunodeficiency virus 1HIV AntibodiesHIV Envelope Protein gp120HIV envelope protein gp120 (135-148)Immunoglobulin Fab FragmentsPeptide FragmentsPolysaccharidesSwainsonine

Identifiers

PMID23708607
PMCPMC4046252
OpenAlexW2094750078

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.