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ARMC3

Armadillo repeat-containing protein 3 · UniProt Q5W041

Length
872 aa
Mass
96.4 kDa
Annotated
2026-06-09
24 papers in source corpus 16 papers cited in narrative 16 extracted findings
Cross-family judge vs UniProt: tie faithfulness: 5/6 claims corpus-supported (83%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ARMC3 (mammalian) and its yeast ortholog Vac8 are armadillo-repeat proteins that act as membrane-anchored scaffolds coupling the vacuolar/lysosomal membrane to autophagic and membrane-inheritance machinery (PMID:31512555, PMID:34705610). Vac8 is targeted to the vacuolar membrane by N-terminal myristoylation, with deletion of the myristoylation site abolishing localization and producing fragmented vacuoles and inheritance defects (PMID:9664035); stable membrane attachment further requires palmitoylation of N-terminal cysteines, a modification installed by the DHHC acyltransferase Pfa3 — whose recognition of Vac8 is conferred specifically by the 11th armadillo repeat — and which adds functional roles beyond mere anchoring (PMID:16301533, PMID:16720644, PMID:19416974). Through its ARM domain, Vac8 anchors the phagophore assembly site to the vacuole by binding Atg13, thereby recruiting the Atg1 initiation complex, and additionally recruits class III PI3K complex I via the Atg14 C-terminus to drive autophagosome biogenesis (PMID:31512555, PMID:32508216, PMID:37436710). The same scaffold supports vacuole inheritance through a tripartite Myo2–Vac17–Vac8 complex [PMID:bio_10.1101_2025.03.24.645041]. These activities are made mutually exclusive by the protein's quaternary state: an intramolecular H1-helix/ARM1 contact governs Vac8 self-association, and Vac17 binding clamps H1 to ARM1 to block dimerization and thereby competitively exclude the Nvj1 and Atg13 interactions (PMID:31512555, PMID:37094131). In mammals, ARMC3 is the functional homolog of Vac8, with its ARM domains recruiting PtdIns3K-CI to initiate autophagosome formation; loss of ARMC3 blocks ribophagy in spermatids, lowers mitochondrial energy, and produces immotile flagella (PMID:34705610). Truncating ARMC3 mutations cause sterilizing sperm tail defects in cattle and asthenozoospermia with disrupted flagellar ultrastructure in humans, establishing ARMC3 as required for normal spermatogenesis (PMID:26923438, PMID:39221575).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 1998 Medium

    Established how Vac8 reaches its site of action and that it is functionally required for vacuole maintenance, answering where this protein works.

    Evidence GFP fusion live imaging and N-terminal myristylation mutant analysis with deletion genetics in yeast

    PMID:9664035

    Open questions at the time
    • Did not resolve the molecular partners through which Vac8 directs inheritance
    • Role of additional lipid modifications not yet defined
  2. 2005 Medium

    Identified that Vac8 also undergoes palmitoylation and that this modification is required for vacuole fusion, distinguishing lipid anchoring from fusion function.

    Evidence In vitro vacuole fusion assay on purified yeast vacuoles with antibody inhibition and complex analysis; DHHC deletion mutant analysis identifying Pfa3

    PMID:15701652 PMID:16301533

    Open questions at the time
    • Direct enzyme-substrate mechanism of Pfa3 on Vac8 not yet reconstituted
    • Whether palmitoylation has roles separable from fusion unresolved
  3. 2006 Medium

    Dissected which Vac8 modifications and domains support which functions, separating membrane anchoring from inheritance, Cvt transport, and pexophagy.

    Evidence Cysteine and domain-deletion mutagenesis with vacuolar inheritance, Cvt, and pexophagy (alcohol oxidase) readouts in yeast and Pichia pastoris

    PMID:16720644 PMID:16874085 PMID:16921262

    Open questions at the time
    • Structural basis of ARM-domain partner recognition not yet defined
    • Identity of all ARM-domain effectors incomplete
  4. 2009 High

    Defined the molecular specificity of Vac8 palmitoylation, showing N-myristoylation primes the reaction and the 11th ARM repeat dictates Pfa3 recognition.

    Evidence In vitro palmitoylation assay with chimeric proteins and competition/truncation mutants

    PMID:19416974

    Open questions at the time
    • In vivo dynamics of sequential modification not addressed
    • Whether mammalian ARMC3 is similarly modified untested here
  5. 2019 High

    Provided the structural logic of how Vac8 self-association and Atg13 binding underlie distinct autophagy pathways, explaining functional partitioning.

    Evidence X-ray crystallography of Vac8-Atg13, AUC, ITC, SAXS with in vivo assays; complementary ITC/CD lipid-binding analysis of Atg13

    PMID:31352862 PMID:31512555

    Open questions at the time
    • How upstream signals switch Vac8 quaternary state not defined
    • Mammalian structural conservation untested
  6. 2020 Medium

    Showed Vac8 anchors the phagophore assembly site to the vacuole by recruiting the Atg1 initiation complex via Atg13, defining its role in autophagy initiation.

    Evidence VAC8 deletion and auxin-inducible degradation with fluorescence microscopy and autophagy activity assays in yeast

    PMID:32508216

    Open questions at the time
    • Quantitative contribution of Vac8 anchoring versus other PAS tethers unresolved
    • Regulation of PAS positioning by signals not addressed
  7. 2023 High

    Resolved how PI3K complex I is brought to the PAS through Vac8 and how Vac17 enforces mutual exclusivity among Vac8 functions.

    Evidence Co-IP with deletion mutants and autophagy flux assays for the Atg14-Vac8 interaction; crystal structure of Vac8-Vac17 with mutagenesis and in vivo inheritance assays

    PMID:37094131 PMID:37436710

    Open questions at the time
    • Temporal coordination of competing partner binding in vivo not mapped
    • How the cell selects between inheritance and autophagy states unclear
  8. 2021 Medium

    Established mammalian ARMC3 as the functional Vac8 homolog and linked its autophagy function to spermatogenesis, bridging yeast mechanism to mammalian physiology.

    Evidence Armc3 knockout mice with ribophagy and mitochondrial assays plus yeast complementation

    PMID:34705610

    Open questions at the time
    • Direct biochemical demonstration of ARMC3 partner binding in mammalian cells limited
    • Subcellular membrane anchor of ARMC3 in spermatids not defined
  9. 2024 Medium

    Connected ARMC3 loss-of-function to human disease, showing truncating variants cause asthenozoospermia with flagellar and mitochondrial ultrastructural defects.

    Evidence Bovine homozygosity mapping/whole-genome sequencing of tail-stump defect; human whole-exome sequencing, RT-PCR, Western blot, and TEM of patient sperm

    PMID:26923438 PMID:39221575

    Open questions at the time
    • No functional rescue confirming causality in human cells
    • Mechanism linking autophagy defect to flagellar disassembly not directly demonstrated
  10. 2025 Low

    Structurally defined the Myo2-Vac17-Vac8 transport complex, clarifying how Vac8 couples to myosin V for vacuole inheritance.

    Evidence Cryo-EM with AlphaFold prediction, genetics, and transport assays (preprint)

    PMID:bio_10.1101_2025.03.24.645041

    Open questions at the time
    • Preprint, not peer reviewed
    • Vac8-Vac17 linkage inferred partly from structure prediction
    • Mammalian relevance of the transport complex untested

Open questions

Synthesis pass · forward-looking unresolved questions
  • How ARMC3-dependent autophagy is mechanistically required for mammalian flagellar assembly and what regulates the switch between its competing scaffolding states remains open.
  • No direct mammalian biochemistry of ARMC3 partner recruitment
  • Signal controlling Vac8/ARMC3 quaternary state unknown
  • Causal chain from ribophagy block to flagellar defect undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 4 GO:0008092 cytoskeletal protein binding 1
Localization
GO:0005773 vacuole 3
Pathway
R-HSA-9612973 Autophagy 4 R-HSA-9609507 Protein localization 1
Partners
ATG11ATG13ATG14MYO2NVJ1PFA3VAC17YKT6
Complex memberships
Myo2-Vac17-Vac8 vacuole inheritance complexVac8-Atg13-Atg1 initiation complexVac8-PI3K complex I (via Atg14)

Evidence

Reading pass · 16 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1998 Yeast Vac8 (ARMC3 ortholog) localizes to the vacuolar membrane via N-terminal myristylation; deletion of the myristylation site abolishes vacuolar localization. Loss of Vac8 causes accumulation of small fragmented vacuoles and defective vacuolar inheritance. GFP fusion live imaging, N-terminal myristylation mutant analysis, deletion genetics Journal of cell science Medium 9664035
2005 Vac8 palmitoylation on isolated yeast vacuoles is mediated by the R-SNARE Ykt6 and is part of a SNARE subcomplex distinct from the Nyv1-containing complex; this reaction is ATP-independent, restricted to a narrow time window, and stimulated by EDTA (ion chelation). Palmitoylation is required for vacuole fusion. In vitro vacuole fusion assay with purified vacuoles, antibody inhibition, protein complex analysis The Journal of biological chemistry Medium 15701652
2005 The DHHC palmitoyl acyltransferase Pfa3 is specifically required for efficient vacuolar localization of Vac8 in vivo; Pfa3 deletion impairs Vac8 palmitoylation and reduces vacuole fusion, while vacuole morphology and inheritance appear normal. DHHC deletion mutant analysis, in vivo localization, vacuole fusion assay Proceedings of the National Academy of Sciences of the United States of America Medium 16301533
2006 Stable vacuolar membrane binding of Vac8 requires two N-terminal cysteines for palmitoylation regardless of their combination; palmitoylation adds functional roles beyond membrane anchoring — a basic-residue replacement mutant that still localizes to vacuoles can support cytoplasm-to-vacuole transport but requires at least one palmitoylation cysteine for vacuolar morphology and inheritance functions. Cysteine mutagenesis, vacuolar inheritance assay, Cvt pathway assay, fluorescence microscopy Journal of cell science Medium 16720644
2006 In Pichia pastoris, Vac8 ARM repeat domains (central region) are required for formation of vacuolar arm-like extensions that engulf peroxisomes during micropexophagy, and Vac8 is essential for recruitment of Atg11 to the vacuolar membrane during glucose-induced pexophagy; palmitoylation/myristoylation sites are required for protein stability and vacuolar association. Domain deletion mutants, GFP localization, pexophagy assay (alcohol oxidase activity), genetic knockouts Autophagy Medium 16921262
2006 In Pichia pastoris, the ARM repeat domain of Vac8 is required for vacuolar inheritance but not for micropexophagy; deletion of both ARM and C-terminal domains abolishes vacuolar sequestering membrane formation and abolishes recruitment of Atg11 to the vacuolar membrane during micropexophagy. Domain deletion mutants, fluorescence microscopy, vacuolar inheritance assay Autophagy Medium 16874085
2009 Pfa3 palmitoylates each of the three N-terminal cysteines of Vac8 in vitro, with efficiency enhanced by prior N-myristoylation; the 11th armadillo repeat of Vac8 is a key determinant for specific recognition by Pfa3, as shown by chimeric protein and competition experiments. In vitro palmitoylation assay, chimeric protein analysis, competition assay with truncation mutants The Journal of biological chemistry High 19416974
2019 Crystal structure of Vac8 bound to Atg13 reveals that the Atg13 extended loop (70 Å) binds the ARM domain of Vac8 in an antiparallel manner; the N-terminal H1 helix of Vac8 intramolecularly associates with ARM1 and regulates Vac8 self-association (dimerization), which is required differentially for Cvt and PMN autophagy pathways. Different quaternary structures of Vac8 (Atg13-bound heterotetramer vs. Nvj1-bound complex) mediate distinct autophagic functions. X-ray crystallography, analytical ultracentrifugation, isothermal titration calorimetry, SAXS, in vivo functional assays Autophagy High 31512555
2019 The Atg13 C-terminus binds lipid membranes via electrostatic interactions and hydrophobic insertion of a Phe residue; this phospholipid binding and Vac8 binding are mutually exclusive because they involve overlapping residues in the Atg13 IDR, and both interactions are required for efficient autophagy. Isothermal titration calorimetry, circular dichroism, lipid-binding assays, mutagenesis Autophagy Medium 31352862
2020 Vac8 anchors the phagophore assembly site (PAS) to the vacuolar membrane by binding Atg13 and thereby recruiting the Atg1 initiation complex; VAC8 deletion or Vac8 mislocalization reduce autophagy activity, establishing Vac8 as required for correct vacuolar localization of the PAS. VAC8 deletion, auxin-inducible protein degradation (AID), fluorescence microscopy, autophagy activity assay Autophagy Medium 32508216
2016 A 1 bp frameshift deletion (p.A451fs26) in bovine ARMC3 that truncates the protein by 401 amino acids (46%) is causally associated with a sterilizing tail stump sperm defect characterized by severely disorganized, immotile spermatozoa tails, establishing ARMC3 as required for normal spermatogenesis. Homozygosity mapping, whole-genome re-sequencing, segregation analysis in affected bulls BMC genetics Medium 26923438
2021 Mouse ARMC3 is the functional homolog of yeast Vac8; its ARM domains recruit PtdIns3K-CI (class III PI3K complex I) to the phagophore assembly site to initiate autophagosome formation via PtdIns3P generation. Armc3 knockout mice show blocked ribophagy in spermatids, low mitochondrial energy levels, immotile flagella, and male infertility. Mouse knockout, ribophagy assay, mitochondrial function assay, yeast complementation studies Autophagy Medium 34705610
2023 X-ray crystal structure of the Vac8-Vac17 complex reveals a bipartite interaction interface; binding of Vac17 to Vac8 clamps the H1 helix to ARM1, preventing Vac8 dimerization and thereby competitively inhibiting Vac8 interactions with Nvj1 and Atg13. Mutation of key interface residues severely impairs vacuole inheritance in vivo. X-ray crystallography, mutagenesis, binding affinity measurements, in vivo vacuole inheritance assay Proceedings of the National Academy of Sciences of the United States of America High 37094131
2023 PI3KCI interacts with the vacuolar membrane anchor Vac8 via the Atg14 C-terminal region in a constitutive manner; this interaction cooperates with Atg38-Atg1 complex and Vps30-Atg9 interactions to target PI3KCI to the PAS for autophagosome biogenesis. Co-immunoprecipitation, deletion mutant analysis, autophagy flux assays, genetic epistasis The Journal of cell biology Medium 37436710
2024 A homozygous splicing variant (c.916+1G>A) in human ARMC3 causes exon 8 skipping, producing a truncated protein undetectable by Western blot in patient sperm, and results in asthenozoospermia with disrupted flagellar ultrastructure including vacuolated sperm mitochondria at the midpiece. Whole-exome sequencing, RT-PCR, Western blot, transmission electron microscopy of patient sperm Clinical genetics Medium 39221575
2025 The vacuole-specific adaptor Vac17 interacts with Myo2 (yeast myosin V) through two distinct binding sites (handhold mechanism); cryo-EM and structure prediction show one of these sites links to Vac8 on the vacuole membrane, forming the Myo2-Vac17-Vac8 complex for vacuole transport to daughter cells. Cryo-electron microscopy, AlphaFold structure prediction, genetic analysis, cell-based transport assays bioRxivpreprint Low bio_10.1101_2025.03.24.645041

Source papers

Stage 0 corpus · 24 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1998 YEB3/VAC8 encodes a myristylated armadillo protein of the Saccharomyces cerevisiae vacuolar membrane that functions in vacuole fusion and inheritance. Journal of cell science 65 9664035
2005 The DHHC protein Pfa3 affects vacuole-associated palmitoylation of the fusion factor Vac8. Proceedings of the National Academy of Sciences of the United States of America 51 16301533
2009 Molecular recognition of the palmitoylation substrate Vac8 by its palmitoyltransferase Pfa3. The Journal of biological chemistry 45 19416974
2006 Palmitoylation determines the function of Vac8 at the yeast vacuole. Journal of cell science 44 16720644
2016 A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) cattle. BMC genetics 34 26923438
2023 The Atg1 complex, Atg9, and Vac8 recruit PI3K complex I to the pre-autophagosomal structure. The Journal of cell biology 28 37436710
2020 Vac8 determines phagophore assembly site vacuolar localization during nitrogen starvation-induced autophagy. Autophagy 27 32508216
2006 Candida albicans VAC8 is required for vacuolar inheritance and normal hyphal branching. Eukaryotic cell 25 16467476
2006 Role of Vac8 in formation of the vacuolar sequestering membrane during micropexophagy. Autophagy 24 16874085
2019 Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways. Autophagy 20 31512555
2005 ATP-independent control of Vac8 palmitoylation by a SNARE subcomplex on yeast vacuoles. The Journal of biological chemistry 19 15701652
2019 The carboxy terminus of yeast Atg13 binds phospholipid membrane via motifs that overlap with the Vac8-interacting domain. Autophagy 16 31352862
2006 Early and late molecular events of glucose-induced pexophagy in Pichia pastoris require Vac8. Autophagy 16 16921262
2023 Chemical Complementarity of Breast Cancer Resident, T-Cell Receptor CDR3 Domains and the Cancer Antigen, ARMC3, is Associated With Higher Levels of Survival and Granzyme Expression. Cancer informatics 13 37313373
2019 Vac8 Controls Vacuolar Membrane Dynamics during Different Autophagy Pathways in Saccharomyces cerevisiae. Cells 13 31262095
2021 A conserved Vac8/ARMC3-PtdIns3K-CI cascade regulates autophagy initiation and functions in spermiogenesis by promoting ribophagy. Autophagy 11 34705610
2024 A homozygous ARMC3 splicing variant causes asthenozoospermia and flagellar disorganization in a consanguineous family. Clinical genetics 10 39221575
2023 Structures of Vac8-containing protein complexes reveal the underlying mechanism by which Vac8 regulates multiple cellular processes. Proceedings of the National Academy of Sciences of the United States of America 7 37094131
2022 The Expansion of the Spectrum in Stuttering Disorders to a Novel ARMC Gene Family (ARMC3). Genes 6 36553564
2006 Cloning and expression of ARMC3_v2, a novel splicing variant of the human ARMC3 gene. Genetika 3 16915934
2024 The emerging significance of Vac8, a multi-purpose armadillo-repeat protein in yeast. Autophagy 2 39045779
2025 The vacuolar protein 8 (Vac8) homolog in Cryptococcus neoformans plays conserved and unique roles in vacuolar and cellular morphology, impacting important stress responses and virulence traits. bioRxiv : the preprint server for biology 0 40661350
2025 The Vacuolar Protein 8 (Vac8) Homolog in Cryptococcus neoformans Impacts Stress Responses and Virulence Traits Through Conserved and Unique Roles. Journal of fungi (Basel, Switzerland) 0 41440702
2023 Erratum to "Chemical Complementarity of Breast Cancer Resident, T-Cell Receptor CDR3 Domains and the Cancer Antigen, ARMC3, is Associated With Higher Levels of Survival and Granzyme Expression". Cancer informatics 0 37465006

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