Affinage

VPS35L

VPS35 endosomal protein-sorting factor-like · UniProt Q7Z3J2

Length
963 aa
Mass
109.6 kDa
Annotated
2026-06-11
28 papers in source corpus 15 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 8/8 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

VPS35L (C16orf62) is the central scaffolding subunit of an endosomal recycling machinery that returns internalized transmembrane proteins to the cell surface and prevents their lysosomal degradation (PMID:28892079). It is the core component of the Retriever heterotrimer (VPS35L–VPS26C–VPS29), a complex that is biochemically distinct from retromer and that couples with the CCC and WASH complexes to recycle α5β1 integrin and over 120 cell surface proteins (PMID:28892079). Cryo-EM structures show that Retriever assembles through a mechanism unlike its retromer paralog, and that VPS35L sits within the larger Commander supercomplex as part of a Retriever–DENND10 effector module scaffolded by CCDC22 and CCDC93 onto a COMMD1-10 core (PMID:38062209, PMID:38459129). VPS35L is the shared subunit bridging Retriever and the CCC complex (PMID:31537807, PMID:36353989), and cargo recognition is mediated by SNX17, which binds directly at the VPS35L–VPS26C interface in a reaction activated both by cargo engagement and by SNX17 association with PI(3)P membranes (PMID:39653850). Within the CCC complex, VPS35L participates in regulating endosomal PI(3)P levels and WASH-dependent F-actin, controlling receptor retention versus recycling (PMID:31537807), and supports trafficking of the copper transporter ATP7A (PMID:25355947). Physiologically, VPS35L is required to maintain cell surface LDLR and LRP1, and its loss reduces LDL uptake and raises plasma cholesterol (PMID:36353989, PMID:36113987). Biallelic loss-of-function variants in VPS35L cause 3C/Ritscher-Schinzel-like syndrome, with a missense variant that abolishes Retriever assembly, impaired autophagy in knockout cells, and embryonic lethality in homozygous knockout mice (PMID:31712251). VPS35L is also exploited by pathogens, supporting HPV16 retrograde trafficking via direct binding of the L2 capsid protein and enabling coronavirus entry by maintaining surface levels of the receptor APN (PMID:33177206, PMID:39222358).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2014 High

    Before VPS35L was assigned to any complex, it was unclear how COMMD/CCDC proteins linked to endosomal trafficking; this work placed C16orf62 within the CCC complex tethered to endosomes via WASH subunit FAM21 and required for ATP7A copper-dependent trafficking.

    Evidence Co-immunoprecipitation, siRNA knockdown, fluorescence microscopy and copper homeostasis assays in human cells

    PMID:25355947

    Open questions at the time
    • Did not resolve whether C16orf62 has a distinct second complex beyond CCC
    • No structural basis for assembly
    • Cargo repertoire beyond ATP7A undefined
  2. 2017 High

    It was unknown how cargo internalized via SNX17 escaped lysosomal degradation; this study defined the Retriever heterotrimer (VPS35L–VPS26C–VPS29) as a retromer-distinct machine that, with SNX17, CCC, and WASH, recycles integrin and >120 surface proteins.

    Evidence Reciprocal Co-IP, quantitative proteomics, and siRNA knockdown with cargo recycling readouts

    PMID:28892079

    Open questions at the time
    • Molecular mechanism of SNX17–Retriever coupling not resolved
    • No structure of the complex
    • Direct versus indirect SNX17 contacts unclear
  3. 2019 High

    The functional relationship between CCC and Retriever was undefined; this work established VPS35L as the shared subunit and showed CCC integrity (not Retriever) controls endosomal PI(3)P via MTMR2, governing WASH/F-actin and receptor retention.

    Evidence Co-IP, siRNA knockdown, phosphoinositide measurements, imaging of endosomal F-actin and receptors

    PMID:31537807

    Open questions at the time
    • Mechanism by which CCC controls MTMR2 phosphorylation incomplete
    • How shared VPS35L is partitioned between complexes unknown
  4. 2019 High

    Whether VPS35L disruption causes human disease was unknown; biallelic loss-of-function variants were shown to cause Ritscher-Schinzel-like syndrome, with a missense allele abolishing Retriever assembly, impaired autophagy, and embryonic lethality in null mice.

    Evidence Exome sequencing, Co-IP complex-formation assay, knockout mouse, autophagy flux assays

    PMID:31712251

    Open questions at the time
    • Mechanistic link between Retriever loss and autophagy defect not detailed
    • Tissue-specific contributions to syndrome phenotypes unresolved
  5. 2018 High

    How endosomal recycling controls plasma lipids was unclear; in vivo work showed the CCC core including C16orf62 is required to maintain surface LDLR and LRP1, and its destabilization causes hypercholesterolaemia.

    Evidence Liver-specific COMMD knockout mice, CRISPR/Cas9 somatic CCDC22 editing, targeted proteomics, surface receptor measurements

    PMID:29545368

    Open questions at the time
    • Direct role of VPS35L versus COMMD/CCDC partners not isolated here
    • Receptor selectivity mechanism undefined
  6. 2021 Medium

    It was unknown whether Retriever is hijacked during viral entry; HPV16 L2 was shown to bind VPS35L directly to recruit Retriever during retrograde genome trafficking.

    Evidence Co-IP of L2 with Retriever subunits, siRNA knockdown infectivity assay, colocalization imaging

    PMID:33177206

    Open questions at the time
    • Binding interface on VPS35L not mapped
    • Single lab, no structural validation
  7. 2022 High

    The specific contributions of VPS35L versus VPS26C to lipoprotein receptor trafficking were unresolved; in vivo deletions showed VPS35L loss reduces both LDLR and LRP1 and raises cholesterol, whereas VPS26C loss selectively affects LRP1.

    Evidence Somatic CRISPR/Cas9 liver-specific editing in mice, surface biotinylation, plasma lipid and proteomic analyses

    PMID:36113987 PMID:36353989

    Open questions at the time
    • Why VPS35L and VPS26C differ in receptor selectivity unexplained
    • Patient-cell LDL uptake endpoint relies on single method per readout
  8. 2023 High

    The structural basis of Retriever assembly was unknown; cryo-EM revealed a unique assembly distinct from retromer and showed cancer-associated VPS35L mutations disrupt complex formation and membrane protein homeostasis.

    Evidence Cryo-EM, AlphaFold modeling, Co-IP, proteomics, trafficking assays, variant mutagenesis

    PMID:37333304 PMID:37397996 PMID:38062209

    Open questions at the time
    • Cargo-bound conformations not captured
    • Dynamics of CCC coupling at atomic resolution incomplete
  9. 2024 High

    The architecture of the full higher-order assembly was undefined; cryo-EM of the endogenous 16-protein Commander complex placed the VPS35L Retriever module with DENND10 on a CCDC22/CCDC93-scaffolded COMMD1-10 core and linked it to cilium and centrosome functions.

    Evidence Cryo-EM of endogenous complex, mass spectrometry proteomics, interaction mapping

    PMID:38459129

    Open questions at the time
    • Functional consequences of cilium/centrosome association not mechanistically dissected
    • Stoichiometry dynamics in cells unresolved
  10. 2024 High

    How SNX17 recruits Retriever to endosomes was unknown; reconstitution showed SNX17 binds the VPS35L–VPS26C interface, with the interaction activated both by cargo binding relieving autoinhibition and by PI(3)P membrane association.

    Evidence Biophysical assays with recombinant proteins, structure-guided mutagenesis, liposome binding

    PMID:39653850

    Open questions at the time
    • In vivo validation of the dual-activation model limited
    • Quantitative contribution of each input to recruitment unmeasured
  11. 2024 Medium

    Whether VPS35L mediates other viral entry routes was open; a genome-wide screen showed VPS35L knockout reduces coronavirus entry by lowering surface levels of the receptor APN, without direct spike interaction.

    Evidence Genome-wide CRISPR/Cas9 screen, knockout validation, virus binding/internalization assays, surface APN quantification

    PMID:39222358

    Open questions at the time
    • Whether APN is a direct Retriever cargo not established
    • Single host-cell system
  12. 2026 Medium

    The physiological breadth of Retriever recycling was extending; VPS35L deficiency was shown to impair LRP1 surface expression and Siglec-15 ligand maintenance, blocking osteoclast differentiation.

    Evidence Genome-wide CRISPR/Cas9 knockout screen, flow cytometry of surface receptors, osteoclast differentiation assay

    PMID:41569849

    Open questions at the time
    • Direct cargo relationship between Retriever and Siglec-15 ligands not biochemically confirmed
    • In vivo bone phenotype not tested

Open questions

Synthesis pass · forward-looking unresolved questions
  • How VPS35L is partitioned between the CCC and Retriever assemblies within the Commander supercomplex, and how this partitioning sets cargo selectivity in different tissues, remains unresolved.
  • No mechanism defining cargo-specific routing
  • Tissue-specific regulation of complex assembly unknown
  • Structural basis of CCC–Retriever switching incomplete

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2 GO:0060090 molecular adaptor activity 2
Localization
GO:0005768 endosome 2 GO:0005886 plasma membrane 2
Pathway
R-HSA-1643685 Disease 2 R-HSA-5653656 Vesicle-mediated transport 2 R-HSA-9609507 Protein localization 2
Partners
CCDC22CCDC93DENND10FAM21SNX17VPS26CVPS29
Complex memberships
CCC complexCommander complexRetriever

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2017 VPS35L (C16orf62) is a core subunit of the Retriever complex, a heterotrimer composed of DSCR3 (VPS26C), C16orf62 (VPS35L), and VPS29. Retriever is biochemically and functionally distinct from retromer, associates with the cargo adaptor SNX17, and couples with CCC and WASH complexes to prevent lysosomal degradation and promote cell surface recycling of α5β1 integrin and over 120 cell surface proteins. Co-immunoprecipitation, quantitative proteomic analysis, siRNA knockdown with cargo recycling readout, biochemical fractionation Nature cell biology High 28892079
2019 CCC and Retriever complexes are closely linked through sharing VPS35L as a common subunit. The integrity of CCC, but not Retriever, is required to maintain normal endosomal levels of PI(3)P; CCC depletion leads to elevated PI(3)P, enhanced WASH activation, excess endosomal F-actin, and trapping of internalized receptors. CCC regulates phosphorylation and endosomal recruitment of the PI(3)P phosphatase MTMR2. Co-immunoprecipitation, siRNA knockdown, phosphoinositide measurements, fluorescence imaging of endosomal F-actin and receptor trafficking Nature communications High 31537807
2023 Cryo-EM structure of the human Retriever complex (VPS35L, VPS26C, VPS29) at high resolution reveals a unique assembly mechanism distinct from its paralog retromer. AlphaFold predictions combined with biochemical, cellular, and proteomic analyses elucidate how the Retriever-CCC supercomplex is organized and show that cancer-associated mutations in VPS35L disrupt complex formation and impair membrane protein homeostasis. Cryogenic electron microscopy, AlphaFold structural prediction, biochemical co-immunoprecipitation, quantitative proteomics, cell-based membrane protein trafficking assays, mutagenesis of cancer-associated variants Nature structural & molecular biology High 38062209
2023 Cryo-EM structure of Retriever (VPS35L, VPS26C, VPS29) and structural organization of the entire Retriever-CCC complex established, with cancer-associated mutations shown to disrupt complex formation. (Preprint version of PMID:38062209.) Cryogenic electron microscopy, AlphaFold predictions, biochemical and proteomic analyses bioRxivpreprint High 37333304 37397996
2024 Structure of the 16-protein Commander complex determined by cryo-EM and mass spectrometry-based proteomics reveals that VPS35L is part of the Retriever subcomplex (with VPS26C and VPS29), which together with DENND10 forms an effector module scaffolded by CCDC22 and CCDC93 onto a stable COMMD1-10 core. Major interaction interfaces are defined, and a strong association with cilium assembly and centrosome/centriole functions is uncovered. Cryogenic electron microscopy of endogenous complex, mass spectrometry-based proteomics, biochemical interaction mapping Nature structural & molecular biology High 38459129
2019 Biallelic loss-of-function variants in VPS35L (compound heterozygous frameshift + missense) cause 3C/Ritscher-Schinzel-like syndrome. The missense variant (p.Ala919Thr) specifically abolishes Retriever complex formation. VPS35L knockout cells show decreased autophagic function under nutrient-rich, starvation, and Torin 1 conditions. Vps35l homozygous knockout mice are embryonic lethal between E7.5 and E10.5. Exome sequencing, co-immunoprecipitation (complex formation assay), knockout mouse generation, autophagy flux assays (LC3-II/p62), cellular loss-of-function Journal of medical genetics High 31712251
2014 C16orf62 (VPS35L) is part of the CCC complex (COMMD/CCDC22/CCDC93/C16orf62) that is linked to early endosomes via interaction with the WASH complex subunit FAM21. This assembly is required for endosomal trafficking of the copper transporter ATP7A; CCC component depletion prevents copper-dependent movement of ATP7A from endosomes. Co-immunoprecipitation, siRNA knockdown, fluorescence microscopy of endosomal localization, copper homeostasis assays Molecular biology of the cell High 25355947
2022 VPS35L is a shared subunit between Retriever and CCC complexes in hepatocytes. Liver-specific VPS35L deletion reduces VPS26C levels, minimally impacts CCC composition, decreases cell surface LDLR and LRP1, and raises plasma cholesterol by ~21%. In contrast, VPS26C deletion does not affect VPS35L or CCC, but selectively impairs LRP1 (not LDLR) trafficking and delays postprandial triglyceride clearance. Somatic CRISPR/Cas9 liver-specific gene editing in mice, cell surface biotinylation, plasma lipid measurements, quantitative proteomics of complex composition Arteriosclerosis, thrombosis, and vascular biology High 36353989
2022 VPS35L ablation in patient-derived cells decreases cell surface levels of LRP1 and LDLR, resulting in reduced LDL cellular uptake, establishing the molecular mechanism of hypercholesterolaemia in VPS35L-associated Ritscher-Schinzel syndrome. Patient-derived cell lines, flow cytometry for cell surface receptor levels, LDL uptake assay Journal of medical genetics Medium 36113987
2018 C16orf62 (VPS35L) is part of the core CCC complex (CCDC22, CCDC93, C16orf62); COMMD protein deficiency destabilizes this core complex and reduces cell surface LDLR and LRP1, leading to hypercholesterolaemia. CCDC22 deletion via CRISPR/Cas9 somatic editing similarly destabilizes the entire CCC complex including C16orf62. Liver-specific knockout mice (Commd1/6/9), CRISPR/Cas9 somatic gene editing (Ccdc22), quantitative targeted proteomics, cell surface receptor measurements Circulation research High 29545368
2021 HPV16 L2 minor capsid protein directly interacts with the C16orf62 (VPS35L) subunit of Retriever during infection, in a manner similar to L2's interaction with VPS35 of retromer. This interaction mediates Retriever recruitment during retrograde trafficking of the viral genome; knockdown of VPS35L impairs HPV infection. Co-immunoprecipitation of L2 with retriever subunits, siRNA knockdown of VPS35L with infectivity readout, colocalization imaging Journal of virology Medium 33177206
2024 C16orf62 (VPS35L) knockout via genome-wide CRISPR/Cas9 screen dramatically reduces binding and internalization of porcine deltacoronavirus (PDCoV) into host cells, and this effect is mediated through downregulation of the PDCoV receptor APN (aminopeptidase N) at the cell surface, consistent with VPS35L's role in endosomal recycling. No direct interaction between C16orf62 and the viral spike protein was detected. Genome-wide CRISPR/Cas9 library screen, gene knockout validation, virus binding/internalization assays, cell surface APN quantification Emerging microbes & infections Medium 39222358
2024 SNX17 directly interacts with Retriever through its C-terminal region binding the interface of VPS35L and VPS26C subunits. This interaction is enhanced by SNX17 cargo binding (which relieves an intramolecular autoinhibitory interaction) and by SNX17 binding to PI(3)P-containing membranes, revealing dual activation mechanisms for Retriever recruitment to endosomes. Biophysical assays with recombinant proteins, structural model-guided mutagenesis, liposome binding assays EMBO reports High 39653850
2026 VPS35L (Vps35l) deficiency in RAW264.7 cells impairs LRP1 expression at the plasma membrane and impairs osteoclast differentiation, demonstrating that Retriever-mediated endosome-to-plasma membrane recycling is required for maintenance of Siglec-15 ligands and osteoclast precursor function. Genome-wide knockout screen (CRISPR/Cas9), flow cytometry for Siglec-15 ligand and LRP1 surface levels, osteoclast differentiation assay Cell reports Medium 41569849

Source papers

Stage 0 corpus · 28 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2017 Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling. Nature cell biology 282 28892079
2013 Identification of driver genes in hepatocellular carcinoma by exome sequencing. Hepatology (Baltimore, Md.) 245 23728943
2014 COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Molecular biology of the cell 186 25355947
2019 Towards a molecular understanding of endosomal trafficking by Retromer and Retriever. Traffic (Copenhagen, Denmark) 148 30993794
2018 The COMMD Family Regulates Plasma LDL Levels and Attenuates Atherosclerosis Through Stabilizing the CCC Complex in Endosomal LDLR Trafficking. Circulation research 107 29545368
2019 Endosomal PI(3)P regulation by the COMMD/CCDC22/CCDC93 (CCC) complex controls membrane protein recycling. Nature communications 97 31537807
2009 Methylation of CLDN6, FBN2, RBP1, RBP4, TFPI2, and TMEFF2 in esophageal squamous cell carcinoma. Oncology reports 49 19288010
2023 Structural organization of the retriever-CCC endosomal recycling complex. Nature structural & molecular biology 38 38062209
2024 Structure and interactions of the endogenous human Commander complex. Nature structural & molecular biology 35 38459129
2019 Biallelic VPS35L pathogenic variants cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex. Journal of medical genetics 35 31712251
2013 Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma. World journal of gastroenterology 22 24379610
2021 Human Papillomavirus 16 L2 Recruits both Retromer and Retriever Complexes during Retrograde Trafficking of the Viral Genome to the Cell Nucleus. Journal of virology 21 33177206
2019 DNA methylation changes that precede onset of dysplasia in advanced sessile serrated adenomas. Clinical epigenetics 21 31200767
2022 Clinical diversity and molecular mechanism of VPS35L-associated Ritscher-Schinzel syndrome. Journal of medical genetics 19 36113987
2021 Commander Complex-A Multifaceted Operator in Intracellular Signaling and Cargo. Cells 17 34943955
2022 Cargo-Specific Role for Retriever Subunit VPS26C in Hepatocyte Lipoprotein Receptor Recycling to Control Postprandial Triglyceride-Rich Lipoproteins. Arteriosclerosis, thrombosis, and vascular biology 14 36353989
2024 Genome-wide CRISPR/Cas9 library screen identifies C16orf62 as a host dependency factor for porcine deltacoronavirus infection. Emerging microbes & infections 13 39222358
2019 Ancestral reconstruction of protein interaction networks. PLoS computational biology 13 31658251
2012 An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination. BMC genomics 11 22793670
2022 Expanding the pre- and postnatal phenotype of WASHC5 and CCDC22 -related Ritscher-Schinzel syndromes. European journal of medical genetics 9 36130690
2024 Selective cargo and membrane recognition by SNX17 regulates its interaction with Retriever. EMBO reports 8 39653850
2020 Circular RNA circ_C16orf62 Suppresses Cell Growth in Gastric Cancer by miR-421/Tubulin beta-2A Chain (TUBB2A) Axis. Medical science monitor : international medical journal of experimental and clinical research 7 33006960
2023 Circ-C16orf62 Regulates Oxidized low-density Lipoprotein-induced Apoptosis, Inflammation, Oxidative Stress and Cholesterol Accumulation of Macrophages via Mediating RAB22A Expression by Targeting miR-377. Applied biochemistry and biotechnology 3 36892682
2025 CCDC22 mutations that impair COMMD binding cause attenuated 3C/Ritscher-Schinzel syndrome. BMC medical genomics 1 40448120
2023 Peripheral Blood-Derived CircVPS35L as a Potential Diagnostic Biomarker for Non-Small Cell Lung Cancer. Oncology 1 37307805
2023 Structural Organization of the Retriever-CCC Endosomal Recycling Complex. bioRxiv : the preprint server for biology 1 37333304
2023 Structural Organization of the Retriever-CCC Endosomal Recycling Complex. Research square 1 37397996
2026 Comprehensive identification of the genes involved in the expression of Siglec-15 ligands on osteoclast precursors. Cell reports 0 41569849

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