Evidence map›Paper›PMID 40593686›Full record

ArticleNature communications2025

HIV-1 vif mediates ubiquitination of the proximal protomer in the APOBEC3H dimer to induce degradation.

Katarzyna A Skorupka, Kazuhiro Matsuoka, Bakar Hassan, Rodolfo Ghirlando, Vanivilasini Balachandran, Ting-Hua Chen, Kylie J Walters, Celia A Schiffer, Matthias Wolf, Yasumasa Iwatani and 1 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. 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

11 authors.

Katarzyna A Skorupka *Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA.ORCID http://orcid.org/0000-0002-6631-6011
Kazuhiro Matsuoka *Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan.
Bakar HassanProtein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.ORCID http://orcid.org/0000-0003-2079-6387
Rodolfo GhirlandoLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, 20892-0540, USA.
Vanivilasini BalachandranCancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA.
Ting-Hua ChenMolecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID http://orcid.org/0000-0001-8104-0562
Kylie J WaltersProtein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.ORCID http://orcid.org/0000-0001-7590-2891
Celia A SchifferDepartment of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.ORCID http://orcid.org/0000-0003-2270-6613
Matthias WolfMolecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID http://orcid.org/0000-0001-8480-0918
Yasumasa IwataniClinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan. yasumasa.iwatani@nnh.go.jp.ORCID http://orcid.org/0000-0001-9269-4828
Hiroshi MatsuoCancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA. hiroshi.matsuo@nih.gov.ORCID http://orcid.org/0000-0002-4559-6157

Funding

WORK ORDER 126643 B539 EXPAND IC SUITE75N91019D00024 · NIAID · LEIDOS BIOMEDICAL RESEARCH, INC. · PI BRISCOE, LYNN · 2019 to 2025
$3932.6M
Myosin VI: a new ubiquitin receptorZIABC011627 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI WALTERS, KYLIE · 2015 to 2025
$4.6M
Structurally dissecting APOBEC3's for HIV-1 restriction and beyondR01AI150478 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI SCHIFFER, CELIA A. · 2019 to 2024
$3.9M
Intramural NIH HHS ZIA BC011627Japan Agency for Medical Research and Development (AMED) JP17fk0410304Japan Agency for Medical Research and Development (AMED) JP23fk0410058h0001NCI NIH HHS 75N91019D00024NIAID NIH HHS R01 AI150478U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER) R01AI150478
6 · The paper itself

Abstract

The APOBEC3 family of cytidine deaminases restricts retroviruses like HIV-1 by mutating viral DNA. HIV-1 evades this restriction by producing Vif, which recruits the Cullin-5 (CUL5) E3 ubiquitin ligase complex to promote APOBEC3 degradation. Here we resolve key aspects of this counter-defense mechanism by determining a 3.6 Å cryo-EM structure of chimpanzee APOBEC3H (cpzA3H) in complex with HIV-1 Vif and three components of the CUL5 E3 ligase-CBFβ, EloB, and EloC (VCBC). The structure captures cpzA3H as an RNA-mediated dimer within the cpzA3H-VCBC complex, allowing us to examine the role of dimerization. We find that ubiquitination occurs specifically at two lysine residues on the Vif-proximal protomer, while the distal protomer remains unmodified. The structural model of the active cpzA3H-Vif-CUL5 E3 ligase holoenzyme reveals spatial preferences for ubiquitin transfer to the targeted lysine residues. These findings enhance our understanding of A3H degradation and suggest new antiviral strategies targeting this host-virus interface.

Indexed as

AminohydrolasesHIV-1vif Gene Products, Human Immunodeficiency VirusAnimalsCore Binding Factor beta SubunitCryoelectron MicroscopyCullin ProteinsElonginHumansLysineModels, MolecularProtein MultimerizationProteolysisUbiquitinationUbiquitin-Protein LigasesAminohydrolasesAPOBEC3H protein, humanCore Binding Factor beta SubunitCUL5 protein, humanCullin ProteinsELOB protein, humanELOC protein, humanElonginLysineUbiquitin-Protein Ligasesvif Gene Products, Human Immunodeficiency Virusvif protein, Human immunodeficiency virus 1

Identifiers

PMID40593686
PMCPMC12217271

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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.