Evidence map›Paper›PMID 40960494›Full record

ArticleeLife2025

Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response.

C J San Felipe, Jyoti Batra, Monita Muralidharan, Shivali Malpotra, Durga Anand, Rachel Bauer, Kliment A Verba, Danielle L Swaney, Nevan J Krogan, Michael Grabe and 1 more

Abstract read
In one paragraph

Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

C J San FelipeDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0002-2695-5951
Jyoti BatraQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0002-2335-0607
Monita MuralidharanQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, San Francisco, United States.
Shivali MalpotraQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, San Francisco, United States.
Durga AnandQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, San Francisco, United States.
Rachel BauerQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, San Francisco, United States.
Kliment A VerbaQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0002-2238-8590
Danielle L SwaneyQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0001-6119-6084
Nevan J KroganQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0003-4902-337X
Michael GrabeDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0003-3509-5997
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0002-5080-2859

Funding

Targeting Viroporins and Coronavirus M ProteinU19AI171110 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James Solomon Fraser · 2022 to 2026
$103.4M
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI Gregory L Hura · 2017 to 2026
$28.6M
Bio-Organic Biomedical Mass Spectromy ResourceP41GM103481 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BURLINGAME, ALMA L · 2012 to 2015
$6.4M
Equipment for Discovering and Manipulating Macromolecular Conformational EnsemblesR35GM145238 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James Solomon Fraser · 2022 to 2026
$3.1M
Ion permeation, lipid flipping, and membrane remodeling by TMEM16 proteinsR01GM137109 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GRABE, MICHAEL · 2021 to 2024
$1.4M
National Institute of Allergy and Infectious Diseases U19AI171110NIAID NIH HHS U19 AI171110NIGMS NIH HHS GM145238NIGMS NIH HHS P30 GM124169NIGMS NIH HHS P41 GM103481NIGMS NIH HHS R01 GM137109NIGMS NIH HHS R01GM137109NIGMS NIH HHS R35 GM145238
6 · The paper itself

Abstract

Open Reading Frame 9b (Orf9b), an accessory protein of SARS-CoV and -2, is involved in innate immune suppression through its binding to the mitochondrial receptor Translocase of Outer Membrane 70 (Tom70). Previous structural studies of Orf9b in isolation revealed a β-sheet-rich homodimer; however, structures of Orf9b in complex with Tom70 revealed a monomeric helical fold. Here, we developed a biophysical model that quantifies how Orf9b switches between these conformations and binds to Tom70, a requirement for suppressing the type 1 interferon response. We used this model to characterize the effect of lipid binding and mutations in variants of concern to the Orf9b:Tom70 equilibrium. We found that the binding of a lipid to the Orf9b homodimer biases the Orf9b monomer:dimer equilibrium towards the dimer by reducing the dimer dissociation rate ~100 fold. We also found that mutations in variants of concern can alter different microscopic rate constants without significantly affecting binding to Tom70. Together, our results highlight how perturbations to different steps in these coupled equilibria can affect the apparent affinity of Orf9b to Tom70, with potential downstream implications for interferon signaling in coronavirus infection.

Indexed as

InterferonsInterferon Type ISARS-CoV-2COVID-19HumansMitochondrial Precursor Protein Import Complex ProteinsMutationProtein BindingProtein MultimerizationInterferonsInterferon Type IMitochondrial Precursor Protein Import Complex ProteinsTOMM70 protein, humanbiochemistrychemical biologycoronavirusE. colihumanOrf9bTom70

Identifiers

PMID40960494
PMCPMC12443476

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.