PXD039492-1

PXD039492 is an original dataset announced via ProteomeXchange.

Title	Proximity labelling reveals intracristal quality control in mitochondria
Description	The intracristal space (ICS) is a distinct subdomain of the mitochondrial intermembrane space (IMS) where oxidative phosphorylation occurs. This region supposedly controls the dynamic demands regulating mitochondrial respiration; however, its other molecular components remain largely unknown. To remedy this, we developed isotope-coded desthiobiotin-phenol probes that enabled differential mass analysis of post-translocated modifications. Using this unique proximity labelling approach dubbed “iSpot-ID”, we discovered that TMEM177 is exclusively localised to the ICS and that the protein offers an ICS targeting modality for studying the unique characteristics of ICS, such as the local pH, redox states, and temperature in the space. Furthermore, we obtained a proteome specifically localised to the ICS using iSpot-ID with TMEM177-APEX2, which included a high portion of mitochondrial matrix-targeting proteins and several known IMS-localised proteases as well as subunits of the OXPHOS complex. This protein accumulation was enriched by inhibiting the import of mitochondrial matrix proteins or by inducing other stress conditions; the protein was consequently degraded by proteases in the ICS. Our data revealed that the ICS is important for mitochondrial quality control under dynamic cellular states.
HostingRepository	PRIDE
AnnounceDate	2025-07-02
AnnouncementXML	Submission_2025-07-01_19:49:15.447.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sanghee Shin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue; monohydroxylated residue
Instrument	Orbitrap Eclipse; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-16 13:54:08	ID requested
⏵ 1	2025-07-01 19:49:15	announced

Dataset with its publication pending

submitter keyword: Human, APEX2, mitochondria, cristae, proximity labelling

Jong-Seo Kim
contact affiliation	School of Biological Sciences, Seoul National University, Seoul 08826, Korea Center for RNA Research, Institute of Basic Science, Seoul 08826, Korea
contact email	jongseokim@snu.ac.kr
lab head
Sanghee Shin
contact affiliation	Dana-Farbar Cancer Institute Harvard Medical School
contact email	sunnyshin54@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD039492

PRIDE project URI

• PRIDE
  1. PXD039492
     1. Label: PRIDE project
     2. Name: Proximity labelling reveals intracristal quality control in mitochondria