Evidence map›Paper›PMID 29304101›Full record

ArticlePLoS pathogens2018

Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors.

Jennifer M Binning, Amber M Smith, Judd F Hultquist, Charles S Craik, Nathalie Caretta Cartozo, Melody G Campbell, Lily Burton, Florencia La Greca, Michael J McGregor, Hai M Ta and 6 more

Open access · goldAbstract read
In one paragraph

Article in PLoS pathogens, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
2.1field-weighted citation impact, top 14% 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

16 citing papers in PubMed, 24 citations in OpenAlex.

  1. Review
  2. Article
  3. Review
  4. Article
  5. Article
  6. Review
  7. Article
  8. Characterization of an A3G-VifMolecular & cellular proteomics : MCP · 2021
    Article
  9. Article
  10. Article
  11. Article
  12. Why recombinant antibodies - benefits and applications.Current opinion in biotechnology · 2019
    Review
  13. Article
  14. Review
  15. Article
  16. Article
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

16 authors at 3 institutions in 1 country.

Jennifer M BinningDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.ORCID 0000-0001-5871-686X
Amber M SmithKeck Advanced Microscopy Laboratory and Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America.
Judd F HultquistJ. David Gladstone Institutes, San Francisco, California, United States of America.
Charles S CraikDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.ORCID 0000-0001-7704-9185
Nathalie Caretta CartozoDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.
Melody G CampbellKeck Advanced Microscopy Laboratory and Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America.
Lily BurtonDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.
Florencia La GrecaDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.
Michael J McGregorJ. David Gladstone Institutes, San Francisco, California, United States of America.
Hai M TaDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.
Koen BartholomeeusenDepartment of Medicine, University of California, San Francisco, California, United States of America.
B Matija PeterlinDepartment of Medicine, University of California, San Francisco, California, United States of America.
Nevan J KroganJ. David Gladstone Institutes, San Francisco, California, United States of America.
Natalia SevillanoDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.
Yifan ChengKeck Advanced Microscopy Laboratory and Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America.ORCID 0000-0001-9535-0369
John D GrossDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America.ORCID 0000-0002-1377-4705
University of California, San Francisco · USHoward Hughes Medical Institute · USQB3 · US

Funding

Virology CoreP30AI027763 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STEVEN Grant DEEKS · 1988 to 2026
$93.6M
X-ray Screening and Rapid Structure DeterminationP50GM082250 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FRANKEL, ALAN D · 2007 to 2018
$48.8M
Virus CoreU19AI106754 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ALBRECHT, RANDY A. · 2013 to 2017
$26.0M
Molecular Virology and Systems Biology Screening CoreP01AI090935 · NIAID · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI HOFFMANN, ALEXANDER · 2010 to 2014
$20.4M
Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
Structure and Function of the Decapping Enzyme ComplexR01GM078360 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GROSS, JOHN D · 2009 to 2018
$2.5M
TAT TransactivationR01AI125104 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI PETERLIN, BORIS MATIJA · 2016 to 2020
$2.0M
Linux cluster for near atomic resolution single particle cryo-EMS10OD020054 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2015 to 2015
$456k
Developing Small Molecule Screens for Vif-APOBEC3 antagonistsR21AI118528 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GROSS, JOHN D · 2015 to 2016
$396k
Evolution of the Vif E3 Ubiquitin LigaseF32AI120867 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BINNING, JENNIFER · 2016 to 2018
$141k
Structural Investigation into the HIV RNA Nuclear Export ComplexF32GM123536 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SMITH, AMBER MARIE · 2016 to 2018
$113k
NIAID NIH HHS F32 AI120867NIAID NIH HHS P01 AI090935NIAID NIH HHS P30 AI027763NIAID NIH HHS R01 AI125104NIAID NIH HHS R21 AI118528NIAID NIH HHS T32 AI060537NIAID NIH HHS U19 AI106754NIGMS NIH HHS F32 GM123536NIGMS NIH HHS P50 GM082250NIGMS NIH HHS R01 GM078360NIH HHS F32-AI120867NIH HHS F32-GM123536NIH HHS P01 AI090935NIH HHS P30 AI027763NIH HHS R21AI118528NIH HHS S10 OD020054NIH HHS S10OD020054NIH HHS U19 AI106754
6 · The paper itself

Abstract

The lentiviral protein Viral Infectivity Factor (Vif) counteracts the antiviral effects of host APOBEC3 (A3) proteins and contributes to persistent HIV infection. Vif targets A3 restriction factors for ubiquitination and proteasomal degradation by recruiting them to a multi-protein ubiquitin E3 ligase complex. Here, we describe a degradation-independent mechanism of Vif-mediated antagonism that was revealed through detailed structure-function studies of antibody antigen-binding fragments (Fabs) to the Vif complex. Two Fabs were found to inhibit Vif-mediated A3 neutralization through distinct mechanisms: shielding A3 from ubiquitin transfer and blocking Vif E3 assembly. Combined biochemical, cell biological and structural studies reveal that disruption of Vif E3 assembly inhibited A3 ubiquitination but was not sufficient to restore its packaging into viral particles and antiviral activity. These observations establish that Vif can neutralize A3 family members in a degradation-independent manner. Additionally, this work highlights the potential of Fabs as functional probes, and illuminates how Vif uses a multi-pronged approach involving both degradation dependent and independent mechanisms to suppress A3 innate immunity.

Indexed as

Antiviral AgentsAPOBEC DeaminasesCullin ProteinsCytidine DeaminaseCytosine DeaminaseHEK293 CellsHIV-1HIV InfectionsHumansImmunoglobulin Fab FragmentsUbiquitinUbiquitinationvif Gene Products, Human Immunodeficiency VirusVirus AssemblyAntiviral AgentsAPOBEC3 proteins, humanAPOBEC DeaminasesCullin ProteinsCytidine DeaminaseCytosine DeaminaseImmunoglobulin Fab FragmentsUbiquitinvif Gene Products, Human Immunodeficiency Virusvif protein, Human immunodeficiency virus 1

Identifiers

PMID29304101
PMCPMC5773222
OpenAlexW2782324548

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.