Affinage

ANKS3

Ankyrin repeat and SAM domain-containing protein 3 · UniProt Q6ZW76

Length
656 aa
Mass
72.0 kDa
Annotated
2026-04-28
10 papers in source corpus 9 papers cited in narrative 9 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ANKS3 is a multi-domain scaffold protein that integrates ciliary signaling with post-transcriptional mRNA regulation through its ankyrin repeats, SAM domain, and coiled-coil domain. Its SAM domain forms head-to-tail polymers that recruit ANKS6-SAM to one end, and its coiled-coil domain directly binds Bicc1 to inhibit target mRNA binding, thereby dispersing Bicc1 ribonucleoparticle condensates; ANKS6 modulates ANKS3 conformation to reinstate Bicc1 condensation, establishing an antagonistic ANKS3/ANKS6 switch that governs Bicc1 liquid-to-gel phase transitions and organ laterality (PMID:24998259, PMID:37733651, PMID:37275520). ANKS3 localizes to renal cilia, interacts with nephronophthisis proteins including NPHP1 (which curtails ANKS3 polymerization), and its ankyrin repeats bind and retain Nek7 in the cytoplasm (PMID:25671767, PMID:26188091). ANKS3 also acts downstream of cilia and polycystins to regulate the transcription factor Glis2, linking polycystin signaling to renal homeostasis, as genetic inactivation of Anks3 suppresses cyst progression in Pkd1 mouse models [PMID:bio_10.1101_2025.04.22.649832].

Mechanistic history

Synthesis pass · year-by-year structured walk · 5 steps
  1. 2014 High

    Structural resolution of the ANKS3-SAM polymer and its heterotypic complex with ANKS6-SAM established that ANKS3 self-assembles via head-to-tail SAM polymerization and recruits ANKS6 to one polymer end, and that the disease-causing ANKS6-R823W mutation disrupts this interaction.

    Evidence Crystal structures of ANKS3-SAM polymer and ANKS3-SAM/ANKS6-SAM complex with biochemical binding assays and mutagenesis

    PMID:24998259

    Open questions at the time
    • Functional consequence of ANKS3 polymerization in cells was not addressed
    • No downstream readout linking the ANKS3-ANKS6 interaction to a signaling pathway
    • Polymer length regulation mechanism in vivo was unknown
  2. 2015 Medium

    ANKS3 was placed within the nephronophthisis protein network and shown to localize to cilia; its depletion caused laterality defects and cyst formation in zebrafish, while its interaction with Nek7 via ankyrin repeats regulated Nek7 cytoplasmic retention.

    Evidence Co-immunoprecipitation with NPHPs and Nek7, GFP localization in multi-ciliated cells, zebrafish morpholino knockdown, subcellular fractionation for Nek7 localization

    PMID:25671767 PMID:26188091 PMID:26327442

    Open questions at the time
    • NPHP1's mechanism for curtailing ANKS3 polymerization was not defined molecularly
    • The nature of the ~20 kDa Nek7-dependent modification of ANKS3 remained unresolved
    • Laterality and cyst phenotypes relied on morpholino knockdown without genetic mutant confirmation
  3. 2017 High

    Demonstration that ANKS3, ANKS6, and Bicc1 cooperatively assemble into giant macromolecular complexes in vivo — but neither ANKS3 nor ANKS6 alone formed such structures — established the tripartite nature of the scaffold system.

    Evidence Crystal structure of Bicc1-SAM, co-immunoprecipitation of domain constructs, fluorescence microscopy of complex assembly

    PMID:29290488

    Open questions at the time
    • The functional output of giant complex formation (e.g., mRNA regulation) was not yet tested
    • Stoichiometry and architecture of the tripartite complex were not resolved
  4. 2023 High

    The coiled-coil domain of ANKS3 was identified as the direct inhibitor of Bicc1 mRNA binding, and the antagonistic ANKS3/ANKS6 regulatory switch controlling Bicc1 ribonucleoparticle phase transitions was reconstituted: ANKS3 disperses Bicc1 condensates while ANKS6 co-recruited by ANKS3 reinstates them.

    Evidence In vitro reconstitution, CRISPR-engineered truncation mutants, mRNA decay assays, in vitro phase separation assays, fluorescence microscopy of granule dynamics

    PMID:37275520 PMID:37733651

    Open questions at the time
    • Identity of specific client mRNAs regulated by the ANKS3/ANKS6/Bicc1 switch in vivo is incomplete
    • How ANKS6 changes ANKS3 conformation at a structural level is not resolved at atomic resolution
    • Whether the phase-transition switch operates identically in different tissue contexts (kidney vs. node) is untested
  5. 2025 Medium

    ANKS3 was positioned as a cytosolic effector downstream of cilia and polycystins and upstream of the transcription factor Glis2, with genetic evidence that Anks3 inactivation suppresses polycystic kidney disease progression in Pkd1 models.

    Evidence (preprint) TRAP-RNASeq, conditional Anks3/Pkd1 mouse knockouts, phosphoproteomics

    PMID:bio_10.1101_2025.04.22.649832

    Open questions at the time
    • Preprint not yet peer-reviewed
    • Mechanism by which polycystin-dependent phosphorylation modifies ANKS3 activity is not defined
    • Whether Glis2 regulation requires Bicc1 or represents an independent ANKS3 output is unclear

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the distinct ANKS3 functions — Bicc1 RNP phase regulation, Nek7 retention, NPHP network scaffolding, and polycystin-Glis2 signaling — are integrated in a unified pathway, and which client mRNAs are directly regulated in each tissue context, remain open questions.
  • No full-length ANKS3 structure or cryo-EM model of the tripartite complex exists
  • Tissue-specific knockout phenotypes in mammals are only partially characterized
  • Whether ANKS3 metabolic effects (nucleoside pool regulation) are direct or secondary to ciliary signaling is untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 4 GO:0005198 structural molecule activity 2
Localization
GO:0005829 cytosol 2 GO:0005929 cilium 2
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 2
Partners
ANKS6BICC1HIF1ANNEK7NPHP1
Complex memberships
ANKS3–ANKS6–Bicc1 ribonucleoparticle

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2014 The SAM domain of ANKS3 directly binds the SAM domain of ANKS6; ANKS3-SAM forms head-to-tail polymers and ANKS6-SAM binds to one end of the polymer. Crystal structures of the ANKS3-SAM polymer and ANKS3-SAM/ANKS6-SAM complex were resolved. The disease-causing R823W mutation in ANKS6 dramatically destabilizes the ANKS6 SAM domain, causing loss of ANKS3-SAM interaction. Crystal structure determination, biochemical binding assays, site-directed mutagenesis BMC structural biology High 24998259
2015 Anks3 interacts with multiple nephronophthisis proteins (NPHPs) and with Bicc1 and HIF1AN. In multi-ciliated epidermal cells, GFP-tagged Anks3 localizes to the cilium. In the absence of NPHP1, Anks3 forms large aggregates, indicating that NPHP1 curtails ANKS3 polymerization. Knockdown of anks3 in zebrafish causes ciliary abnormalities, cyst formation, and laterality defects. Co-immunoprecipitation, GFP localization (live imaging/fluorescence microscopy), zebrafish morpholino knockdown with phenotypic readouts Kidney international Medium 25671767
2015 ANKS3 interacts with the NIMA-related kinase Nek7 via its N-terminal ankyrin repeats. In the presence of Nek7, Anks3 undergoes a ~20 kDa molecular weight modification (not caused by Nek7-mediated phosphorylation, as it also occurs with kinase-dead Nek7). Nek7-Anks3 interaction retains Nek7 in the cytoplasm, preventing its nuclear localization. Co-immunoprecipitation, mass spectrometry (phosphoproteomics), kinase-dead mutant analysis, subcellular fractionation/localization Biochemical and biophysical research communications Medium 26188091
2015 ANKS3 and ANKS6 interact through their SAM domains (confirmed by yeast two-hybrid and co-immunoprecipitation), and co-localize in mouse renal cilia in vivo. Knockdown of Anks3 in vivo in mice is associated with increased transcription of vasopressin-induced genes and altered expression of genes involved in cilium structure, apoptosis, and cell proliferation. Yeast two-hybrid, co-immunoprecipitation, in vivo immunofluorescence localization, in vivo LNA antisense knockdown with transcriptomic readouts PloS one Medium 26327442
2017 ANKS3 recruits ANKS6 to Bicc1, and together the three proteins cooperatively generate giant macromolecular complexes in vivo. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo. The Bicc1-SAM polymer crystal structure was determined, showing canonical SAM polymerization with flexible subunit interface orientations. Crystal structure determination of Bicc1-SAM, co-immunoprecipitation/interaction mapping of full-length and domain constructs, fluorescence microscopy for complex assembly Structure (London, England : 1993) High 29290488
2018 Anks3 depletion in murine inner medullary collecting duct (mIMCD-3) cells significantly alters amino acid and purine/pyrimidine metabolism (48 significantly altered metabolites), reduces nucleoside pools, and elevates PARP1 and cleaved PARP1 levels, suggesting a role for Anks3 in DNA damage responses by balancing the intracellular nucleoside pool. GC-MS and LC-MS/MS metabolomics, western blotting for PARP1 after siRNA knockdown Scientific reports Low 29899363
2023 ANKS3 contains a C-terminal coiled-coil domain that interacts with Bicc1 and inhibits binding of target mRNAs. ANKS6 regulates the conformation of ANKS3, which controls this inhibitory interaction. Together, ANKS3 and ANKS6 dually regulate Bicc1 ribonucleoparticle (RNP) assembly and mRNA binding, with ANKS3 dispersing Bicc1 granules and releasing bound mRNAs, while ANKS6 co-recruited by ANKS3 reinstates Bicc1 condensation. AlphaFold structure predictions, in vitro reconstitution (biochemical validation), CRISPR-engineered truncation mutants, mRNA decay assays PLoS biology High 37733651
2023 ANKS3 disperses Bicc1 SAM-domain-nucleated head-to-tail polymers and releases bound client mRNAs, while co-recruitment of ANKS6 by ANKS3 reinstates Bicc1 condensation and ribonucleoparticle assembly. ANKS3 and ANKS6 antagonistically regulate Bicc1 liquid-to-gel phase transitioning of client transcripts. Biochemical assays (co-immunoprecipitation, in vitro phase separation), RNA binding assays, fluorescence microscopy of granule assembly/dispersion iScience High 37275520
2025 Anks3 functions as a cytosolic regulator of cilia-dependent polycystin signaling, acting downstream of cilia and polycystins and upstream of the transcription factor Glis2. Anks3 regulates polycystin-dependent Glis2 expression in vitro and in vivo, and undergoes polycystin-dependent changes in phosphorylation state. Inactivation of Anks3 in Pkd1 mouse models suppresses cyst progression. Translating ribosome affinity purification (TRAP)-RNASeq, conditional mouse knockout (Pkd1 models), in vitro cell-based assays, phosphoproteomics bioRxivpreprint Medium bio_10.1101_2025.04.22.649832

Source papers

Stage 0 corpus · 10 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2014 Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3. BMC structural biology 41 24998259
2015 Anks3 interacts with nephronophthisis proteins and is required for normal renal development. Kidney international 34 25671767
2017 Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6. Structure (London, England : 1993) 22 29290488
2018 Metabolic Phenotyping of Anks3 Depletion in mIMCD-3 cells - a Putative Nephronophthisis Candidate. Scientific reports 20 29899363
2015 Anks3 alters the sub-cellular localization of the Nek7 kinase. Biochemical and biophysical research communications 17 26188091
2016 ANKS3 is mutated in a family with autosomal recessive laterality defect. Human genetics 16 27417436
2015 ANKS3 Co-Localises with ANKS6 in Mouse Renal Cilia and Is Associated with Vasopressin Signaling and Apoptosis In Vivo in Mice. PloS one 11 26327442
2016 Influence of the R823W mutation on the interaction of the ANKS6-ANKS3: insights from molecular dynamics simulation and free energy analysis. Journal of biomolecular structure & dynamics 8 26295479
2023 Bicc1 ribonucleoprotein complexes specifying organ laterality are licensed by ANKS6-induced structural remodeling of associated ANKS3. PLoS biology 5 37733651
2023 Antagonistic interactions among structured domains in the multivalent Bicc1-ANKS3-ANKS6 protein network govern phase transitioning of target mRNAs. iScience 4 37275520