Affinage

ZFYVE27

Protrudin · UniProt Q5T4F4

Length
411 aa
Mass
45.8 kDa
Annotated
2026-06-11
19 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ZFYVE27 (protrudin) is an endoplasmic reticulum-resident peripheral membrane protein that shapes the tubular ER network and tethers ER membrane contact sites to drive directional membrane trafficking and neurite outgrowth (PMID:23969831, PMID:24668814, PMID:31406056). Through hydrophobic intramembrane hairpin domains and interactions with ER-shaping atlastins and reticulons, it regulates the ER sheet-to-tubule balance and stabilizes the tubular ER network where it predominantly localizes (PMID:23969831, PMID:24668814). As a multidomain scaffold bearing a non-canonical FYVE domain that binds phosphatidylinositol 3-phosphate, an FFAT motif, a Rab-binding domain, and a KIF5-interacting domain, protrudin acts as a tethering factor at ER–endosome/lysosome contact sites, inactivating the small GTPase Rab11 and coupling to the kinesin motor KIF5; it partners with the SMP-domain lipid-transfer protein PDZD8 at ER–late endosome/lysosome contacts to position endolysosomes and promote neurite outgrowth (PMID:31406056, PMID:33912962). Oligomerization via its third hydrophobic region (HR3) is required for protrusion formation, and a neuron-specific microexon included by SRRM4-dependent alternative splicing yields a long isoform that more potently drives neurite outgrowth (PMID:22216323, PMID:28106138). Protrudin was identified as a spastin-binding protein, and an HSP-associated mutation impairs spastin binding while increasing protein stability and rendering cells susceptible to ER stress; knockout mice lack HSP signs, indicating the disease mutations act by a gain-of-toxic-function mechanism (PMID:16826525, PMID:24668814, PMID:33172474). Beyond the neural system, protrudin supports endothelial FAK and mTOR/S6K signaling required for cell migration and retinal angiogenesis (PMID:35368213).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2006 High

    Establishing protrudin's first molecular partner answered how a disease-linked protein connects to HSP biology by showing it binds the microtubule-severing protein spastin and that a disease mutation disrupts this interaction.

    Evidence Yeast two-hybrid, reciprocal co-immunoprecipitation, and colocalization in mammalian cells with a disease-associated mutant

    PMID:16826525

    Open questions at the time
    • Functional consequence of the spastin interaction not resolved
    • Mechanism linking mutation to the aberrant tubular pattern unclear
  2. 2011 High

    Defining protrudin as a PI3P-binding peripheral membrane protein that self-oligomerizes via HR3 answered how it acts mechanistically, showing oligomerization is functionally required for protrusion formation.

    Evidence Sucrose gradient centrifugation, Triton X-114 phase separation, lipid-binding assays, and dominant-negative ΔHR3 overexpression

    PMID:22216323

    Open questions at the time
    • Structural basis of HR3-mediated oligomerization not determined
    • Stoichiometry in vivo unknown
  3. 2013 High

    Mapping protrudin's domain architecture and ER-shaping partners answered what cellular structure it builds, placing it as a regulator of tubular ER morphogenesis.

    Evidence Co-immunoprecipitation with atlastins/ER-shaping proteins, domain analysis, and ER morphology assays with live-cell imaging

    PMID:23969831

    Open questions at the time
    • Quantitative contribution of each domain to morphology not separated
    • Direct membrane-bending activity not reconstituted
  4. 2014 High

    An in vivo interactome and topology study answered which HSP-network proteins protrudin engages and how a disease mutation alters protein behavior, revealing increased mutant stability and ER stress susceptibility.

    Evidence Proteomics of purified protrudin complexes from transgenic mouse brain, membrane topology mapping, and ER stress assays

    PMID:24668814

    Open questions at the time
    • Causal link between increased stability and toxicity not established
    • ER stress mechanism not molecularly defined
  5. 2017 High

    Identifying SRRM4-dependent microexon inclusion answered how neurons tune protrudin function, generating a long isoform with enhanced neurite-promoting activity.

    Evidence Splicing assays, SRRM4 knockdown, CRISPR exon deletion, motif mutation, and neurite outgrowth assays in Neuro2A and embryonic stem cells

    PMID:28106138

    Open questions at the time
    • Molecular basis for enhanced activity of the long isoform unknown
    • In vivo relevance of the microexon not tested
  6. 2019 Medium

    Synthesizing prior data framed protrudin as a membrane contact site tether, integrating Rab11 inactivation, ER membrane bending, and KIF5/VAP interactions into one mechanism.

    Evidence Review consolidating organelle fractionation, domain-function, and MCS tethering experiments

    PMID:31406056

    Open questions at the time
    • Review presents no primary data
    • Direct ordering of tethering events not established
  7. 2020 Medium

    A knockout mouse answered whether HSP mutations act by loss or gain of function, showing behavioral abnormalities but no HSP phenotype and pointing to a gain-of-toxic-function disease mechanism.

    Evidence Protrudin knockout mice subjected to a behavioral test battery

    PMID:33172474

    Open questions at the time
    • Molecular pathway underlying behavioral deficits not resolved
    • Toxic gain-of-function mechanism not directly demonstrated
  8. 2021 High

    Identifying PDZD8 as a partner answered how lipids are delivered at protrudin tethers, showing SMP-domain lipid transfer is required for endolysosome positioning and neurite outgrowth.

    Evidence Co-immunoprecipitation, in vitro lipid-binding and lipid-transfer assays, organelle positioning, and knockdown neurite outgrowth readouts

    PMID:33912962

    Open questions at the time
    • Direction and selectivity of in vivo lipid flux unknown
    • Whether protrudin regulates PDZD8 transfer activity unclear
  9. 2022 Medium

    Extending protrudin beyond neurons answered whether it has vascular roles, linking it to FAK and mTOR/S6K signaling required for endothelial migration and retinal angiogenesis.

    Evidence siRNA knockdown with phospho-FAK imaging and mTOR/S6K immunoblotting, tube formation assays, and retinal vascular analysis in knockout mice

    PMID:35368213

    Open questions at the time
    • Direct molecular link between protrudin and FAK activation not defined
    • Whether the contact-site/trafficking function underlies the signaling phenotype unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • How protrudin's gain-of-toxic-function HSP mutations mechanistically cause neurodegeneration, and how its membrane-bending and lipid-transfer tethering activities are coordinated in vivo, remain unresolved.
  • No structural model of the protrudin tethering complex
  • Causal chain from mutant stability/ER stress to neurodegeneration unestablished
  • Physiological substrates of lipid transfer at protrudin MCSs undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0008289 lipid binding 1 GO:0098772 molecular function regulator activity 1
Localization
GO:0005783 endoplasmic reticulum 2
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 2 R-HSA-5653656 Vesicle-mediated transport 2
Partners
ATL1KIF5APDZD8PLP1RAB11AREEP1SPASTVAPA

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2006 ZFYVE27 (protrudin) was identified as a specific spastin-binding protein via yeast two-hybrid screen, and the interaction was validated by in vivo co-immunoprecipitation and colocalization in mammalian cells. A disease-associated mutation in ZFYVE27 severely impairs its interaction with spastin and causes an aberrant intracellular tubular pattern. Yeast two-hybrid, co-immunoprecipitation, colocalization (fluorescence microscopy) American journal of human genetics High 16826525
2011 ZFYVE27 (protrudin) self-interacts via its third hydrophobic region (HR3) and oligomerizes into dimer/tetramer forms as shown by sucrose gradient centrifugation. ZFYVE27 is a peripheral membrane protein that binds phosphatidylinositol 3-phosphate. Deletion of HR3 (ΔHR3) abolishes protrusion formation and acts as a dominant negative over wild-type ZFYVE27, demonstrating that oligomerization is required for neurite extension. Yeast two-hybrid, co-immunoprecipitation, sucrose gradient centrifugation, subcellular fractionation, Triton X-114 phase separation, lipid-binding assay, dominant-negative overexpression PloS one High 22216323
2013 Protrudin (ZFYVE27/SPG33) contains hydrophobic intramembrane hairpin domains, interacts with tubular ER proteins (atlastins and ER-shaping proteins), and functions in ER morphogenesis by regulating the sheet-to-tubule balance and tubule interconnection density. Protrudin also harbors a KIF5-interacting domain, a Rab-binding domain, a non-canonical FYVE domain, and an FFAT domain. Co-immunoprecipitation, domain analysis, ER morphology assays (overexpression/knockdown), live-cell imaging Proceedings of the National Academy of Sciences of the United States of America High 23969831
2014 Protrudin localizes predominantly to the tubular endoplasmic reticulum (ER) and forced expression promotes formation and stabilization of the tubular ER network. One of three hydrophobic segments forms a hydrophobic hairpin domain. Protrudin interacts with multiple HSP-related proteins (SPG2/PLP1, SPG3A/atlastin-1, SPG31/REEP1, REEP5, KIF5A/B/C, reticulon 1/3/4). The HSP-associated mutant protrudin(G191V) has increased intracellular stability and cells expressing it show increased susceptibility to ER stress. Proteomics (purified protrudin complexes from transgenic mouse brain), membrane topology analysis, ER morphology assay, ER stress assay The Journal of biological chemistry High 24668814
2017 SRRM4 regulates alternative splicing of protrudin (ZFYVE27) pre-mRNA to include a neuron-specific microexon (exon L, encoding 7 amino acids) by recognizing a UGC motif upstream of exon L. The resulting long isoform (protrudin-L) is more effective at promoting neurite outgrowth than the short isoform (protrudin-S). Deletion of exon L impairs neurite outgrowth in Neuro2A cells and embryonic stem cells. RT-PCR/splicing assays, SRRM4 knockdown, exon deletion (CRISPR/genome editing), neurite outgrowth assays, motif mutation Scientific reports High 28106138
2019 Protrudin functions as a tethering factor at membrane contact sites (MCSs) between the ER and other organelles. Its roles at MCSs involve inactivation of the small GTPase Rab11, bending of the ER membrane, and functional interactions with motor protein KIF5 and ER protein VAP. Review synthesizing experimental data (organelle fractionation, domain-function studies, MCS tethering assays cited within) Proceedings of the Japan Academy. Series B, Physical and biological sciences Medium 31406056
2020 Protrudin-deficient mice show pleiotropic behavioral abnormalities (hyperactivity, depression-like behavior, attention deficits, impaired fear-conditioning memory) but no HSP signs, indicating that the HSP-associated mutations likely cause neural degeneration through a gain-of-toxic-function rather than loss-of-function mechanism. Knockout mouse generation, battery of behavioral tests Molecular brain Medium 33172474
2021 PDZD8 is a protrudin (ZFYVE27)-interacting protein that acts as a tether at ER–late endosome/lysosome membrane contact sites. PDZD8's SMP domain binds glycerophospholipids and ceramides and can transfer lipids between membranes in vitro, and this lipid transfer activity is required for late endosome/lysosome positioning and neurite outgrowth. Co-immunoprecipitation, in vitro lipid-binding and lipid-transfer assays, organelle positioning assays, knockdown with neurite outgrowth readout Journal of cell science High 33912962
2022 Protrudin knockdown in endothelial cells inhibits FAK activation, disrupts polarized phospho-FAK distribution, causes perinuclear accumulation of mTOR, and decreases VEGF-mediated S6K activation, leading to impaired endothelial cell migration and angiogenesis. Mice with global protrudin deletion show reduced retinal vascular progression. siRNA knockdown, phospho-FAK immunofluorescence, mTOR/S6K immunoblotting, tube formation assay, in vivo retinal vascular analysis in KO mice Cellular and molecular life sciences : CMLS Medium 35368213

Source papers

Stage 0 corpus · 19 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2012 Hereditary spastic paraplegias with autosomal dominant, recessive, X-linked, or maternal trait of inheritance. Journal of the neurological sciences 229 22554690
2006 ZFYVE27 (SPG33), a novel spastin-binding protein, is mutated in hereditary spastic paraplegia. American journal of human genetics 113 16826525
2018 Clinical spectrum and genetic landscape for hereditary spastic paraplegias in China. Molecular neurodegeneration 72 29980238
2013 Protrudin binds atlastins and endoplasmic reticulum-shaping proteins and regulates network formation. Proceedings of the National Academy of Sciences of the United States of America 56 23969831
2014 Protrudin regulates endoplasmic reticulum morphology and function associated with the pathogenesis of hereditary spastic paraplegia. The Journal of biological chemistry 53 24668814
2021 PDZD8-mediated lipid transfer at contacts between the ER and late endosomes/lysosomes is required for neurite outgrowth. Journal of cell science 46 33912962
2017 SRRM4-dependent neuron-specific alternative splicing of protrudin transcripts regulates neurite outgrowth. Scientific reports 39 28106138
2008 Lack of spartin protein in Troyer syndrome: a loss-of-function disease mechanism? Archives of neurology 33 18413476
2018 Protein-protein interactions reveal key canonical pathways, upstream regulators, interactome domains, and novel targets in ALS. Scientific reports 30 30283000
2016 A Subpopulation of Label-Retaining Cells of the Kidney Papilla Regenerates Injured Kidney Medullary Tubules. Stem cell reports 19 27117784
2022 Protrudin regulates FAK activation, endothelial cell migration and angiogenesis. Cellular and molecular life sciences : CMLS 18 35368213
2011 Oligomerization of ZFYVE27 (Protrudin) is necessary to promote neurite extension. PloS one 18 22216323
2008 A novel candidate locus on chromosome 11p14.1-p11.2 for autosomal dominant hereditary spastic paraplegia. Chinese medical journal 13 18364116
2020 Protrudin-deficient mice manifest depression-like behavior with abnormalities in activity, attention, and cued fear-conditioning. Molecular brain 8 33172474
2019 Roles of protrudin at interorganelle membrane contact sites. Proceedings of the Japan Academy. Series B, Physical and biological sciences 6 31406056
2022 Demographic and Genome Wide Association Analyses According to Muscle Mass Using Data of the Korean Genome and Epidemiology Study. Journal of Korean medical science 4 36573383
2008 Refinement of the SPG9 locus on chromosome 10q23.3-24.2 and exclusion of candidate genes. European journal of neurology 4 18394049
2022 MYO1H is a novel candidate gene for autosomal dominant pure hereditary spastic paraplegia. Molecular genetics and genomics : MGG 2 35704118
2026 Causal Association Between Plasma Proteins and Pericarditis: A Mendelian Randomization Study With Therapeutic Target Identification. Mediators of inflammation 0 41674924

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