Affinage

VPS45

Vacuolar protein sorting-associated protein 45 · UniProt Q9NRW7

Length
570 aa
Mass
65.1 kDa
Annotated
2026-06-11
25 papers in source corpus 17 papers cited in narrative 17 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

VPS45 is a Sec1/Munc18 (SM)-family protein that regulates SNARE-mediated vesicle docking and fusion in the endosomal trafficking pathway, originally defined in yeast as a vacuolar protein sorting factor required for targeting Golgi-derived transport vesicles to the prevacuolar/endosomal compartment (PMID:7706396, PMID:9650782). It acts at the same TGN-to-endosome fusion step as the syntaxin/Qa-SNARE Pep12/Tlg2, with which it functions in an allele-specific, pathway-specific manner (PMID:9335586). Mechanistically, rather than clamping its cognate syntaxin in a closed conformation, VPS45 binds Tlg2 (and the mammalian homolog syntaxin-16) through a short N-terminal peptide motif and holds the SNARE in an open conformation, with its domain 3a helical hairpin unfurled to expose the R-SNARE binding site and template SNARE complex assembly (PMID:12110575, PMID:32804076); domain 3a is the functionally critical region for this assembly activity (PMID:38585203). VPS45 cooperates with the Rab5 effector Rabenosyn-5, which bridges activated Rab5 to the fusion machinery, and this Rab5–Rabenosyn-5–VPS45–syntaxin module drives homotypic fusion that forms early endosomes (PMID:17235359, PMID:18685079, PMID:19931244). In mammalian cells VPS45 is required for Rab5-to-Rab7 conversion during endosome maturation and for cargo delivery to lysosomes, and its loss is embryonic lethal in mice and causes aberrant G-CSF receptor trafficking (PMID:33512427). VPS45 stabilizes its binding partners at the protein level—syntaxin and the v-SNARE Snc2 in yeast, and rabenosyn-5/syntaxin-16 in mammalian systems—such that VPS45 loss depletes these partners and impairs β1 integrin recycling, cell migration, ciliary membrane homeostasis, and FAK-AKT signaling (PMID:23166732, PMID:19931244, PMID:29572244, PMID:40540066). Biallelic VPS45 mutations (Thr224Asn, Glu238Lys) destabilize the protein and cause a congenital syndrome featuring neutropenia, impaired neutrophil β1 integrin expression, increased apoptosis, and defects of the endosomal-lysosomal pathway (PMID:23738510, PMID:23599270).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 1994 High

    Established VPS45 as an SM-family member acting in the vacuolar protein sorting pathway, answering where in the cell it functions.

    Evidence Yeast genetic null analysis with subcellular fractionation and EM

    PMID:7706396

    Open questions at the time
    • No molecular partner identified
    • Fusion-versus-targeting role not distinguished mechanistically
  2. 1997 Medium

    Placed Vps45p with the syntaxin Pep12p at a defined TGN-to-endosome fusion step, identifying its likely SNARE partner and pathway specificity.

    Evidence High-copy suppressor screen with allele-specific suppression and negative controls (VPS33)

    PMID:9335586

    Open questions at the time
    • Genetic only — no direct physical interaction shown
    • Did not define the molecular nature of the Vps45–Pep12 interaction
  3. 1998 Medium

    Restricted VPS45 function to the biosynthetic Golgi-to-endosome route and excluded a requirement in the endocytic delivery route, refining its pathway position.

    Evidence Genetic epistasis and trafficking assays in vps45 and vps27 mutants

    PMID:9650782

    Open questions at the time
    • Endocytic role later revised by metazoan studies
    • No biochemical mechanism for route selectivity
  4. 2002 High

    Defined the molecular binding mode—an N-terminal peptide motif holding syntaxin open rather than closed—and extended it to mammalian syntaxin-16, establishing a conserved SM–syntaxin mechanism.

    Evidence NMR and biochemical binding assays across yeast Tlg2 and mammalian syntaxin-16

    PMID:12110575

    Open questions at the time
    • No full-length structure of the complex at this stage
    • Functional consequence for SNARE assembly not yet shown
  5. 2007 High

    Identified Rabenosyn-5 as a direct VPS45 partner and placed VPS45 downstream of Rab5 in early endosome fusion, linking the SM protein to Rab-controlled endosome dynamics.

    Evidence C. elegans Co-IP, EM, and suppression of dominant-active RAB-5(Q78L)

    PMID:17235359

    Open questions at the time
    • Architecture of the Rab5–Rabenosyn-5–VPS45–syntaxin module not resolved
    • Direct versus indirect Rab5 coupling not separated
  6. 2008 High

    Showed Rabenosyn bridges Rab5 to VPS45 and its syntaxin Avalanche at early endosomes in vivo, and that loss of the complex causes loss of epithelial polarity and neoplastic overproliferation, connecting the fusion machinery to tissue homeostasis.

    Evidence Drosophila null mutants with identical EM phenotypes, co-localization, and epistasis

    PMID:18685079

    Open questions at the time
    • Mechanism linking trafficking defect to proliferation control not defined
    • Stoichiometry of the four-protein module unknown
  7. 2009 High

    Demonstrated in mammalian cells that VPS45 stabilizes rabenosyn-5 and syntaxin-16 and is required for β1 integrin recycling and cell migration, establishing partner-stabilization as a functional output.

    Evidence siRNA knockdown with domain-mutant rescue, reciprocal Co-IP, proteasome inhibition, migration assays

    PMID:19931244

    Open questions at the time
    • Whether stabilization is direct chaperoning or assembly-dependent unclear
    • Recycling-step location within endosomal system not pinpointed
  8. 2012 Medium

    Established that VPS45 sets the cellular levels of both its syntaxin (Tlg2) and v-SNARE (Snc2) partners, with Snc2 restoration reversing mutant phenotypes, defining SNARE stabilization as a core conserved function.

    Evidence Yeast vps45Δ null, overexpression, and selective SNARE-restoration rescue with immunoblotting

    PMID:23166732

    Open questions at the time
    • Molecular basis of SNARE stabilization not resolved
    • Single lab; not extended to mammalian v-SNARE
  9. 2013 High

    Identified biallelic VPS45 mutations as the cause of congenital neutropenia with endosomal-lysosomal defects, connecting protein destabilization to human disease and confirming causality by rescue.

    Evidence Patient exome/homozygosity mapping, immunoblotting, zebrafish model, yeast mutation modeling, and transfection rescue

    PMID:23599270 PMID:23738510

    Open questions at the time
    • Cell-type basis of neutrophil specificity not explained
    • Link between trafficking defect and apoptosis/myelofibrosis mechanistically incomplete
  10. 2018 Medium

    Broadened VPS45/Rabenosyn-5 function to ciliary membrane homeostasis, developmental signaling balance, and iron-uptake trafficking, showing the conserved fusion module supplies diverse physiological outputs.

    Evidence C. elegans ciliary marker quantification, zebrafish lens TGFβ/Wnt reporter assays, Cryptococcus deletion-mutant trafficking and localization

    PMID:29572244 PMID:30071112 PMID:30322969

    Open questions at the time
    • Mitochondrial co-localization in Cryptococcus mechanistically unexplained
    • Direct link from endosomal trafficking to TGFβ/Wnt balance not defined
  11. 2020 High

    Solved the structural basis for VPS45 holding Tlg2 in an open conformation via an unfurled domain 3a, explaining how it templates SNARE assembly in contrast to closed-conformation Munc18-1.

    Evidence X-ray crystallography of the Vps45–Tlg2 complex with biochemical reconstitution

    PMID:32804076

    Open questions at the time
    • Full assembled SNARE-template complex not captured structurally
    • Regulation of the open-to-assembly transition unknown
  12. 2021 High

    Established VPS45 as essential for Rab5-to-Rab7 conversion and lysosomal cargo delivery and showed its loss disrupts G-CSF receptor trafficking, providing the mammalian endosome-maturation framework relevant to neutropenia.

    Evidence Mouse knockout (embryonic lethal), siRNA, live imaging, and Rab5/Rab7 marker analysis

    PMID:33512427

    Open questions at the time
    • How VPS45 mechanistically drives Rab conversion is unresolved
    • GCSFR trafficking defect not directly tied to neutrophil loss
  13. 2024 Medium

    Genetic suppression by a domain 3a mutation in the paralog VPS33A confirmed domain 3a as the functionally critical element for SM-protein-mediated SNARE assembly and revealed overlapping but distinct roles among endosomal SM proteins.

    Evidence C. elegans suppressor screen of vps-45 loss-of-function lethality

    PMID:38585203

    Open questions at the time
    • Single method, single lab
    • Biochemical interplay between VPS45 and VPS33A not reconstituted
  14. 2025 Medium

    Linked the VPS45–syntaxin-16–rabenosyn-5 β1 integrin recycling axis to FAK-AKT signaling and tumor growth, extending the trafficking function to oncogenic signaling control.

    Evidence Co-IP, VPS45 knockout/rescue, surface β1 integrin flow cytometry, signaling immunoblotting, and xenograft model in HCC cells

    PMID:40540066

    Open questions at the time
    • Single lab and single cancer context
    • Whether effect is integrin-recycling-specific versus broader trafficking not isolated

Open questions

Synthesis pass · forward-looking unresolved questions
  • How VPS45 mechanistically couples its open-syntaxin templating activity to Rab5-to-Rab7 conversion, and why its loss produces tissue-specific phenotypes such as neutropenia, remain unresolved.
  • No structure of the assembled Rab5–Rabenosyn-5–VPS45–SNARE module
  • Mechanism of Rab conversion control undefined
  • Cell-type basis of disease specificity unexplained

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0098772 molecular function regulator activity 3 GO:0140313 molecular sequestering activity 2
Localization
GO:0005768 endosome 3 GO:0005794 Golgi apparatus 2 GO:0031410 cytoplasmic vesicle 2
Pathway
R-HSA-5653656 Vesicle-mediated transport 3 R-HSA-1643685 Disease 2 R-HSA-9609507 Protein localization 2
Partners
AVLPEP12RBSNSNC2STX16TLG2VPS33A

Evidence

Reading pass · 17 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 Vps45p is a member of the Sec1p/SM protein family required for vacuolar protein sorting; it associates predominantly with a high-speed membrane fraction containing Golgi, transport vesicles and endosomal membranes (not ER, vacuole, or plasma membrane), and loss of Vps45p causes accumulation of vesicle clusters, indicating a role in targeting/fusion of Golgi-derived transport vesicles in the vacuolar protein sorting pathway. Genetic analysis, subcellular fractionation, overexpression, electron microscopy, polyclonal antiserum immunoblotting Journal of cell science High 7706396
1997 Genetic epistasis in yeast shows that VPS45 and PEP12 (syntaxin/t-SNARE homologue) are allele-specific high-copy suppressors of pep7-20 mutant phenotypes, placing Vps45p and Pep12p together in the same TGN-to-endosome vesicle docking/fusion step; overexpression of VPS33 (a different SM protein) could not suppress, demonstrating pathway specificity. High-copy suppressor genetic screen, allele-specific suppression analysis Genetics Medium 9335586
1998 Vps45p is required for fusion of Golgi-derived vesicles with the prevacuolar/endosomal compartment (functions before Vps27p/class E compartment) but is NOT required for delivery of endocytosed proteins from the plasma membrane to the prevacuolar compartment, restricting its function to the biosynthetic/Golgi-to-endosome route. Genetic epistasis, vacuolar morphology analysis, trafficking assays in vps45 and vps27 mutants European journal of cell biology Medium 9650782
2002 NMR and biochemical experiments showed that Tlg2p (yeast TGN syntaxin) does not adopt a closed conformation but instead binds tightly to Vps45p via a short N-terminal peptide motif; this binding mode is shared by mammalian syntaxin 16, confirming syntaxin 16 as the Tlg2p homolog and establishing that N-terminal peptide-mediated SM–syntaxin interaction is a widespread mechanism. Nuclear magnetic resonance (NMR), biochemical binding assays, sequence/structural comparison The EMBO journal High 12110575
2007 In C. elegans, VPS-45 physically interacts with the Rab5 effector Rabenosyn-5 (RABS-5); both are required for endocytic vesicle fusion to form early endosomes; vps-45 and rabs-5 mutants accumulate aberrantly small endosomes and suppress RAB-5(Q78L)-stimulated endosome fusion, placing VPS-45 downstream of RAB-5 and cooperating with RABS-5. Co-immunoprecipitation, genetic epistasis (dominant active RAB-5 suppression), loss-of-function mutant analysis, electron microscopy EMBO reports High 17235359
2008 In Drosophila, Rabenosyn (Rbsn) bridges an interaction between Rab5 and the SM protein Vps45; Vps45's syntaxin target is Avalanche (Avl); Rbsn, Vps45, Avl, and Rab5 null mutants show identical ultrastructural defects (failure of vesicle fusion to form early endosomes) and all four proteins localize specifically to early endosomes; loss of this complex causes loss of epithelial polarity and neoplastic overproliferation. Genetic null mutants, ultrastructural EM analysis, subcellular localization (immunofluorescence), epistasis, co-localization Molecular biology of the cell High 18685079
2009 In mammalian cells, hVps45 directly interacts with Rabenosyn-5 via a novel sequence in Rabenosyn-5; hVps45 depletion reduces Rabenosyn-5 protein levels via proteasomal degradation, and reduces Syntaxin16 expression with altered Syntaxin6 localization, causing impaired β1 integrin recycling and delayed fibroblast cell migration; β1 integrin recycling was rescued by wild-type Rabenosyn-5 but not a Vps45-binding-deficient mutant. siRNA knockdown, rescue with siRNA-resistant constructs, Co-IP, proteasome inhibitor assays, cell migration assays, immunofluorescence Experimental cell research High 19931244
2012 Yeast Vps45 regulates the cellular levels of its SNARE binding partners Tlg2 (syntaxin) and Snc2 (v-SNARE): cells lacking Vps45 have reduced Tlg2 and Snc2 levels; overexpression of Vps45 increases levels of both; selectively restoring Snc2 in vps45 null cells reverses multiple growth phenotypes of vps45 mutants. Genetic null mutant (vps45Δ), overexpression, rescue by selective SNARE restoration, immunoblotting PloS one Medium 23166732
2013 Homozygous mutations in human VPS45 (Thr224Asn or Glu238Lys) reduce VPS45 protein levels and concomitantly reduce levels of its binding partners rabenosyn-5 and syntaxin-16, reduce β1 integrin surface expression on neutrophils and fibroblasts, impair fibroblast motility, increase apoptosis, and cause absence of neutrophils in a zebrafish vps45-deficiency model; transfection with non-mutated VPS45 corrects migration defect and decreases apoptosis. Immunoblotting, immunofluorescence, flow cytometry, fibroblast motility assay, apoptosis assay, zebrafish knockdown model, gene correction (transfection rescue) The New England journal of medicine High 23738510
2013 The Thr224Asn mutation in VPS45 destabilizes Vps45 protein; introduction of the equivalent mutation into yeast also reduces cellular levels of Vps45 and its cognate syntaxin Tlg2, and patient fibroblasts lack lysosomes and platelets lack α-granules, indicating a defect in the endosomal-lysosomal pathway. Homozygosity mapping, exome sequencing, immunoblotting, yeast mutation modeling, electron microscopy (fibroblast organelle analysis) Blood Medium 23599270
2018 In C. elegans, RABS-5 (Rabenosyn-5) and VPS-45 control periciliary vesicle number and levels of early endosome/endocytic markers (WDFY-2, CAV-1) and the ciliopathy membrane receptor PKD-2 (polycystin-2) at cilia; loss of either protein alters cilium length, morphology, ciliary/periciliary membrane volume and sensory behaviour, linking the RABS-5/VPS-45 complex to regulation of ciliary membrane homeostasis via endocytic processing. C. elegans loss-of-function mutants, live fluorescence imaging, behavioral assays, quantification of membrane markers The EMBO journal Medium 29572244
2018 In Cryptococcus neoformans, Vps45 regulates endocytic trafficking and SNARE interactions; a vps45 deletion mutant is impaired in transporting the Cfo1 ferroxidase from plasma membrane to vacuole (high-affinity iron uptake defect), and Vps45-GFP co-localizes with MitoTracker, indicating an unexpected association with mitochondria; vps45 mutant shows altered mitochondrial membrane potential and calcium homeostasis defects. Deletion mutant analysis, GFP fusion localization with MitoTracker, trafficking assays, sensitivity to electron transport inhibitors, membrane potential measurements PLoS pathogens Medium 30071112
2018 In zebrafish vps45 mutants, lens epithelial cells abnormally differentiate into lens fiber cells without reaching the equator; this ectopic differentiation is independent of FGF signaling but mediated through activation of TGFβ signaling and inhibition of canonical Wnt signaling, identifying VPS45-dependent endosome trafficking as a regulator of TGFβ and Wnt pathway balance during lens development. Zebrafish vps45 mutant analysis, pathway-specific inhibitor/activator treatments, reporter assays for TGFβ and Wnt signaling Development (Cambridge, England) Medium 30322969
2020 Crystal/structural analysis of the Vps45–Tlg2 complex shows that Vps45 holds Tlg2 in an open conformation (SNARE motif disengaged from Habc domain, linker region unfolded), with the domain 3a helical hairpin of Vps45 unfurled to expose the R-SNARE binding site for template complex formation; Vps45 can rescue Tlg2 homo-tetramers into stoichiometric Vps45–Tlg2 complexes. This contrasts with Munc18-1 which traps syntaxin-1 in a closed conformation. X-ray crystallography (structure determination), biochemical reconstitution, mutagenesis-implied domain analysis eLife High 32804076
2021 Mammalian VPS45 is essential for Rab5-to-Rab7 conversion during endosome maturation; loss of VPS45 traps cargo in early endosomes and impairs delivery to lysosomes; VPS45 knockout in mice is embryonic lethal; VPS45 deficiency causes aberrant trafficking of the G-CSF receptor (GCSFR) in the endosomal system. Conditional and constitutive mouse knockout, siRNA knockdown, live cell imaging, immunofluorescence, flow cytometry for Rab5/Rab7 markers Blood High 33512427
2024 Genetic suppressor screen in C. elegans shows that a M376I mutation in domain 3a of VPS33A (another SM protein) suppresses temperature-sensitive lethality caused by loss of VPS-45, demonstrating that domain 3a of SM proteins is functionally critical for SNARE complex assembly in endosomal trafficking and that SM proteins in this pathway have overlapping but distinct domain-level functions. Genetic suppressor screen, C. elegans loss-of-function and suppressor mutant analysis microPublication biology Medium 38585203
2025 VPS45 interacts with syntaxin-16 and rabenosyn-5 to facilitate recycling of β1 integrin to the cell membrane in HCC cells, thereby activating FAK-AKT signaling; VPS45 knockout suppresses β1 integrin surface recycling, FAK-AKT signaling, and tumor growth in xenograft models. Co-immunoprecipitation, VPS45 knockout and rescue experiments, flow cytometry for surface β1 integrin, immunoblotting for FAK-AKT signaling, xenograft tumor model Journal of gastroenterology Medium 40540066

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 How Tlg2p/syntaxin 16 'snares' Vps45. The EMBO journal 153 12110575
1994 Mutations in the VPS45 gene, a SEC1 homologue, result in vacuolar protein sorting defects and accumulation of membrane vesicles. Journal of cell science 131 7706396
2013 A congenital neutrophil defect syndrome associated with mutations in VPS45. The New England journal of medicine 104 23738510
2008 Regulation of early endosomal entry by the Drosophila tumor suppressors Rabenosyn and Vps45. Molecular biology of the cell 75 18685079
2013 The Thr224Asn mutation in the VPS45 gene is associated with the congenital neutropenia and primary myelofibrosis of infancy. Blood 58 23599270
1998 Traffic into the prevacuolar/endosomal compartment of Saccharomyces cerevisiae: a VPS45-dependent intracellular route and a VPS45-independent, endocytic route. European journal of cell biology 58 9650782
2007 The SM protein VPS-45 is required for RAB-5-dependent endocytic transport in Caenorhabditis elegans. EMBO reports 52 17235359
2009 Common and distinct roles for the binding partners Rabenosyn-5 and Vps45 in the regulation of endocytic trafficking in mammalian cells. Experimental cell research 47 19931244
2020 SPI1-induced upregulation of lncRNA SNHG6 promotes non-small cell lung cancer via miR-485-3p/VPS45 axis. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 40 32590190
2018 Endosome maturation factors Rabenosyn-5/VPS45 and caveolin-1 regulate ciliary membrane and polycystin-2 homeostasis. The EMBO journal 28 29572244
2018 The Sec1/Munc18 (SM) protein Vps45 is involved in iron uptake, mitochondrial function and virulence in the pathogenic fungus Cryptococcus neoformans. PLoS pathogens 26 30071112
1997 Genetic interactions between a pep7 mutation and the PEP12 and VPS45 genes: evidence for a novel SNARE component in transport between the Saccharomyces cerevisiae Golgi complex and endosome. Genetics 26 9335586
2020 The Sec1/Munc18 protein Vps45 holds the Qa-SNARE Tlg2 in an open conformation. eLife 23 32804076
2021 Mammalian VPS45 orchestrates trafficking through the endosomal system. Blood 21 33512427
2018 How we approach: Severe congenital neutropenia and myelofibrosis due to mutations in VPS45. Pediatric blood & cancer 16 30294941
2015 Severe congenital neutropenia with neurological impairment due to a homozygous VPS45 p.E238K mutation: A case report suggesting a genotype-phenotype correlation. American journal of medical genetics. Part A 16 26358756
2012 The Sec1/Munc18 protein Vps45 regulates cellular levels of its SNARE binding partners Tlg2 and Snc2 in Saccharomyces cerevisiae. PloS one 14 23166732
2017 A novel homozygous VPS45 p.P468L mutation leading to severe congenital neutropenia with myelofibrosis. Pediatric blood & cancer 13 28453180
1997 Molecular cloning of a mammalian homologue of the yeast vesicular transport protein vps45. Biochimica et biophysica acta 5 9106478
2018 Endocytic trafficking factor VPS45 is essential for spatial regulation of lens fiber differentiation in zebrafish. Development (Cambridge, England) 4 30322969
2025 VPS45 Contributes to the Progression of Hepatocellular Carcinoma by Triggering the Wnt/β-Catenin Signaling Pathway. Molecular carcinogenesis 3 39835603
2025 VPS45 promotes the progression of hepatocellular carcinoma by recycling β1 integrin to the cell membrane via the endocytic pathway. Journal of gastroenterology 1 40540066
2020 Periodontal Disease in Two Siblings with VPS45-associated Severe Congenital Neutropenia Type V: A Case Report. International journal of clinical pediatric dentistry 1 33623350
2024 Domain 3a mutation of VPS33A suppresses larval arrest phenotype in the loss of VPS45 in Caenorhabditis elegans. microPublication biology 0 38585203
2023 A humanized Caenorhabditis elegans model for studying pathogenic mutations in VPS45, a protein essential for membrane trafficking, associated with severe congenital neutropenia. microPublication biology 0 38089934

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