ArticleThe EMBO journal2013
Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding.
Article in The EMBO journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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.
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.
Who cites it
44 citing papers in PubMed, 64 citations in OpenAlex.
- High-resolution NMR spectroscopy of proteins in intact mitochondria.Nature chemical biology · 2026Article
- Di-caffeoylquinic acid: a potential inhibitor for amyloid-beta aggregation.Journal of natural medicines · 2024Article
- NEDD4 family ubiquitin ligase AIP4 interacts with Alix to enable HBV naked capsid egress in an Alix ubiquitination-independent manner.PLoS pathogens · 2024Article
- Database-Driven Identification of Structurally Similar Protein-Protein Interfaces.Journal of chemical information and modeling · 2024Article
- Exosomes: Methods for Isolation and Characterization in Biological Samples.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Avidity-Based Method for the Efficient Generation of Monoubiquitinated Recombinant Proteins.Journal of the American Chemical Society · 2023Article
- Split-Chloramphenicol Acetyl Transferase Assay to Study Protein-Protein Interactions and Ubiquitylation inBio-protocol · 2022Article
- Nonlytic cellular release of hepatitis A virus requires dual capsid recruitment of the ESCRT-associated Bro1 domain proteins HD-PTP and ALIX.PLoS pathogens · 2022Article
- Bro1 family proteins harmonize cargo sorting with vesicle formation.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Article
- Tsg101/ESCRT-I recruitment regulated by the dual binding modes of K63-linked diubiquitin.Structure (London, England : 1993) · 2022Article
- Substrate ubiquitination retains misfolded membrane proteins in the endoplasmic reticulum for degradation.Cell reports · 2021Article
- Review
- The E3 Ubiquitin Ligase RNF5 Facilitates SARS-CoV-2 Membrane Protein-Mediated Virion Release.mBio · 2021Article
- Article
- ALIX- and ESCRT-III-dependent sorting of tetraspanins to exosomes.The Journal of cell biology · 2020Article
- Arabidopsis ALIX Regulates Stomatal Aperture and Turnover of Abscisic Acid Receptors.The Plant cell · 2019Article
- ALIX increases protein content and protective function of iPSC-derived exosomes.Journal of molecular medicine (Berlin, Germany) · 2019Article
- A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs).PLoS computational biology · 2018Article
- Inside job: how the ESCRTs release HIV-1 from infected cells.Biochemical Society transactions · 2018Review
- HIV-1 gag recruits PACSIN2 to promote virus spreading.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
Abstract
The ubiquitylation signal promotes trafficking of endogenous and retroviral transmembrane proteins. The signal is decoded by a large set of ubiquitin (Ub) receptors that tether Ub-binding domains (UBDs) to the trafficking machinery. We developed a structure-based procedure to scan the protein data bank for hidden UBDs. The screen retrieved many of the known UBDs. Intriguingly, new potential UBDs were identified, including the ALIX-V domain. Pull-down, cross-linking and E3-independent ubiquitylation assays biochemically corroborated the in silico findings. Guided by the output model, we designed mutations at the postulated ALIX-V:Ub interface. Biophysical affinity measurements using microscale-thermophoresis of wild-type and mutant proteins revealed some of the interacting residues of the complex. ALIX-V binds mono-Ub with a K(d) of 119 μM. We show that ALIX-V oligomerizes with a Hill coefficient of 5.4 and IC(50) of 27.6 μM and that mono-Ub induces ALIX-V oligomerization. Moreover, we show that ALIX-V preferentially binds K63 di-Ub compared with mono-Ub and K48 di-Ub. Finally, an in vivo functionality assay demonstrates the significance of ALIX-V:Ub interaction in equine infectious anaemia virus budding. These results not only validate the new procedure, but also demonstrate that ALIX-V directly interacts with Ub in vivo and that this interaction can influence retroviral budding.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.