Evidence map›Paper›PMID 34389466›Full record

ArticleMolecular & cellular proteomics : MCP2021

Characterization of an A3G-Vif

Robyn M Kaake, Ignacia Echeverria, Seung Joong Kim, John Von Dollen, Nicholas M Chesarino, Yuqing Feng, Clinton Yu, Hai Ta, Linda Chelico, Lan Huang and 3 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular & cellular proteomics : MCP, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
1.0field-weighted citation impact, top 28% 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

8 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. The Molecular Architecture of the Nuclear Basket.bioRxiv : the preprint server for biology · 2024
    Article
  5. Article
  6. Article
  7. Article
  8. Review
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

13 authors at 5 institutions in 2 countries.

Robyn M KaakeDepartment of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA.
Ignacia EcheverriaDepartment of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
Seung Joong KimDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
John Von DollenDepartment of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA.
Nicholas M ChesarinoDivisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Yuqing FengDepartment of Biochemistry, Microbiology, Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
Clinton YuDepartment of Physiology & Biophysics, University of California, Irvine, California, USA.
Hai TaDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.
Linda ChelicoDepartment of Biochemistry, Microbiology, Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
Lan HuangDepartment of Physiology & Biophysics, University of California, Irvine, California, USA.
John GrossQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.
Andrej SaliQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA. Electronic address: sali@salilab.org.
Nevan J KroganDepartment of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA. Electronic address: nevan.krogan@ucsf.edu.
QB3 · USUniversity of California, Irvine · USUniversity of California, San Francisco · USUniversity of Saskatchewan · CAFred Hutch Cancer Center · US

Funding

RESEARCH PROJECT 2U19AI135990 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI JEFFERY S COX · 2018 to 2026
$21.4M
TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI CHAIT, BRIAN T · 2014 to 2023
$18.8M
X-ray Screening and Rapid Structure DeterminationP50AI150476 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KROGAN, NEVAN J · 2019 to 2021
$14.4M
Using Networks to Seed Hierarchical Whole-cell Models of CancerU54CA209891 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI IDEKER, TREY, KROGAN, NEVAN J · 2017 to 2021
$10.9M
Proteomics of the Proteasome Interacting NetworksR01GM074830 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI HUANG, LAN · 2005 to 2022
$6.1M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
Structural dynamics and function of the COP9 signalosomeR01GM130144 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI HUANG, LAN · 2018 to 2021
$1.2M
Reactivation of Innate Immune Response Pathways as Treatment for HIV InfectionF32AI127291 · NIAID · J. DAVID GLADSTONE INSTITUTES · PI KAAKE, ROBYN MIDORI · 2016 to 2018
$178k
NCI NIH HHS U54 CA209891NIAID NIH HHS F32 AI127291NIAID NIH HHS P50 AI150476NIAID NIH HHS U19 AI135990NIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM074830NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R01 GM130144
6 · The paper itself

Abstract

Structural analysis of host-pathogen protein complexes remains challenging, largely due to their structural heterogeneity. Here, we describe a pipeline for the structural characterization of these complexes using integrative structure modeling based on chemical cross-links and residue-protein contacts inferred from mutagenesis studies. We used this approach on the HIV-1 Vif protein bound to restriction factor APOBEC3G (A3G), the Cullin-5 E3 ring ligase (CRL5), and the cellular transcription factor Core Binding Factor Beta (CBFβ) to determine the structure of the (A3G-Vif-CRL5-CBFβ) complex. Using the MS-cleavable DSSO cross-linker to obtain a set of 132 cross-links within this reconstituted complex along with the atomic structures of the subunits and mutagenesis data, we computed an integrative structure model of the heptameric A3G-Vif-CRL5-CBFβ complex. The structure, which was validated using a series of tests, reveals that A3G is bound to Vif mostly through its N-terminal domain. Moreover, the model ensemble quantifies the dynamic heterogeneity of the A3G C-terminal domain and Cul5 positions. Finally, the model was used to rationalize previous structural, mutagenesis and functional data not used for modeling, including information related to the A3G-bound and unbound structures as well as mapping functional mutations to the A3G-Vif interface. The experimental and computational approach described here is generally applicable to other challenging host-pathogen protein complexes.

Indexed as

APOBEC-3G DeaminaseCore Binding Factor beta SubunitCullin ProteinsMass SpectrometryModels, MolecularUbiquitin-Protein Ligasesvif Gene Products, Human Immunodeficiency VirusAPOBEC-3G DeaminaseCore Binding Factor beta SubunitCullin ProteinsUbiquitin-Protein Ligasesvif Gene Products, Human Immunodeficiency Virusvif protein, Human immunodeficiency virus 1architectures of host–pathogen complexescross-linking mass spectrometryintegrative structure modeling

Identifiers

PMID34389466
PMCPMC8459920
OpenAlexW3188330609

What OpenQuestion holds

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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.