PXD062789-1

PXD062789 is an original dataset announced via ProteomeXchange.

Title	A conserved mechanism for the retrieval of polyubiquitinated proteins from cilia
Description	The temporospatial distribution of proteins within cilia is regulated by intraflagellar transport (IFT), wherein molecular trains shuttle between the cell body and cilium. Defects in this process impair various signal-transduction pathways and cause ciliopathies. Although K63-linked ubiquitination appears to trigger protein export from cilia, the mechanisms coupling polyubiquitinated proteins to IFT remain unclear. Using quantitative proteomics, we identified that a complex of CFAP36, a conserved ciliary protein of previously unknown function, and ARL3, a small GTPase involved in ciliary import, binds polyubiquitinated proteins and links them to retrograde IFT trains. CFAP36 uses a coincidence detection mechanism to simultaneously bind two IFT subunits accessible only in retrograde trains. Depleting CFAP36 accumulates K63-linked ubiquitin in cilia and disrupts Hedgehog signaling, a pathway reliant on the retrieval of ubiquitinated receptors. These findings advance our understanding of ubiquitin-mediated protein transport and ciliary homeostasis, and demonstrate how structural changes in IFT trains achieve cargo selectivity.
HostingRepository	PRIDE
AnnounceDate	2026-06-29
AnnouncementXML	Submission_2026-06-29_09:30:25.573.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD062789
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Robyn Eisert
SpeciesList	scientific name: Chlamydomonas reinhardtii; NCBI TaxID: NEWT:3055; scientific name: Leishmania tarentolae; NCBI TaxID: NEWT:5689; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: NEWT:9825;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-09 15:39:57	ID requested
⏵ 1	2026-06-29 09:30:26	announced

10.6019/PXD062789;

10.1016/j.cell.2025.07.043;

Lange SM, Bennett JA, Eisert RJ, Brown A, A conserved mechanism for the retrieval of polyubiquitinated proteins from cilia. Cell, 188(23):6492-6508.e18(2025) [pubmed]

submitter keyword: Intraflagellar Transport, Flagella, Hedgehog signaling, Ubiquitin,Cilia

Alan Brown
contact affiliation	Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
contact email	alan_brown@hms.harvard.edu
lab head
Robyn Eisert
contact affiliation	Harvard Medical School
contact email	robyn_eisert@hms.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062789
     1. Label: PRIDE project
     2. Name: A conserved mechanism for the retrieval of polyubiquitinated proteins from cilia