Affinage

ANKS3

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

Length
656 aa
Mass
72.0 kDa
Annotated
2026-06-09
10 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ANKS3 is a ciliary ankyrin-repeat and SAM-domain scaffold protein that nucleates and tunes macromolecular assemblies governing left-right axis determination and renal homeostasis (PMID:29290488, PMID:27417436). Through its SAM domain it self-polymerizes and binds the SAM domain of ANKS6, which docks onto one end of the ANKS3-SAM polymer; the disease-associated R823W mutation in ANKS6 abolishes this interaction (PMID:24998259). ANKS3 bridges ANKS6 to Bicc1, and together the three proteins cooperatively build giant SAM-dependent assemblies that neither ANKS3 nor ANKS6 forms alone (PMID:29290488). Within these assemblies ANKS3 acts as a conformational switch over Bicc1-dependent mRNA regulation: a C-terminal coiled-coil of ANKS3 binds Bicc1 and inhibits target mRNA binding, while ANKS6 relieves this inhibition, and ANKS3 disperses Bicc1 condensates to release client transcripts whereas ANKS6 co-recruitment reinstates condensation and ribonucleoparticle phase transitioning (PMID:37733651, PMID:37275520). This regulation controls symmetric versus asymmetric decay of Dand5 mRNA, the basis of ANKS3's role in laterality, and a homozygous loss-of-function ANKS3 variant causes human laterality defects (PMID:27417436, PMID:37733651). ANKS3 also interacts with multiple nephronophthisis proteins, localizes to cilia, and retains the kinase Nek7 in the cytoplasm via its N-terminal ankyrin repeats, with NPHP1 limiting ANKS3 polymerization (PMID:25671767, PMID:26188091). In the kidney ANKS3 acts as a cytosolic regulator of polycystin-dependent cilia signaling, functioning downstream of polycystins but upstream of Glis2; its inactivation suppresses cyst progression in Pkd1 mouse models [PMID:bio_10.1101_2025.04.22.649832].

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2014 High

    Established the structural basis of the core ANKS3-ANKS6 interaction, defining how these scaffolds physically associate and why a disease mutation disrupts it.

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

    PMID:24998259

    Open questions at the time
    • Did not establish the cellular or physiological consequence of the interaction
    • No full-length protein context or in vivo assembly state
  2. 2015 Medium

    Placed ANKS3 in the ciliary nephronophthisis interactome and showed loss-of-function causes ciliopathy phenotypes in vivo, linking the scaffold to cilia and laterality.

    Evidence Co-IP with NPHPs/Bicc1/HIF1AN, GFP ciliary localization, zebrafish morpholino knockdown

    PMID:25671767

    Open questions at the time
    • Morpholino phenotypes not confirmed with genetic mutants in this study
    • Mechanism by which NPHP1 curtails ANKS3 polymerization undefined
  3. 2015 Medium

    Identified ANKS3 as a cytoplasmic retention factor for Nek7, assigning a distinct ankyrin-repeat-mediated function separate from its SAM-domain scaffolding.

    Evidence Co-IP, mass spectrometry, kinase-dead Nek7 mutant, subcellular fractionation

    PMID:26188091

    Open questions at the time
    • Identity of the ~20 kDa ANKS3 modification not determined
    • Functional consequence of Nek7 sequestration not tested in vivo
  4. 2015 Medium

    Confirmed the ANKS3-ANKS6 interaction by orthogonal methods and demonstrated in vivo renal ciliary co-localization and transcriptional impact of ANKS3 loss.

    Evidence Yeast two-hybrid, Co-IP, mouse kidney immunofluorescence, LNA knockdown with transcriptional profiling

    PMID:26327442

    Open questions at the time
    • Transcriptional changes are downstream readouts, not direct mechanism
    • Single-lab in vivo knockdown without genetic confirmation
  5. 2016 Medium

    Provided human and animal genetic evidence that ANKS3 is causally required for right-left axis determination.

    Evidence Human autozygome/exome sequencing, zebrafish WT vs. mutant RNA rescue, CRISPR mutant zebrafish line

    PMID:27417436

    Open questions at the time
    • Molecular mechanism connecting the variant to laterality not resolved in this study
    • Single family/single lab
  6. 2017 High

    Defined the assembly hierarchy showing ANKS3 recruits ANKS6 to Bicc1 to cooperatively form giant complexes, establishing ANKS3 as the bridging scaffold.

    Evidence Bicc1-SAM crystal structure, domain-mapping with truncations, in vivo co-localization

    PMID:29290488

    Open questions at the time
    • Functional output of the giant assemblies not directly tested here
    • Stoichiometry in physiological conditions unresolved
  7. 2023 Medium

    Revealed ANKS3 as a conformational regulator of Bicc1 mRNA binding, mechanistically linking the scaffold to Dand5 transcript fate and laterality.

    Evidence AlphaFold prediction with biochemical validation, in vitro reconstitution, CRISPR truncation animal model

    PMID:37733651

    Open questions at the time
    • Conformational switch model rests on structural prediction plus biochemistry
    • Single-lab novel mechanism
  8. 2023 Medium

    Showed ANKS3 and ANKS6 exert dual opposing control over Bicc1 condensate phase transitioning and mRNA release, defining the biophysical basis of regulation.

    Evidence In vitro reconstitution, RNA-binding assays, condensate imaging

    PMID:37275520

    Open questions at the time
    • Largely in vitro; in-cell condensate dynamics not fully established
    • Single lab
  9. 2025 Medium

    Positioned ANKS3 in the polycystin signaling axis as a cytosolic regulator downstream of cilia/polycystins and upstream of Glis2, with therapeutic relevance to cystic disease.

    Evidence TRAP-RNAseq, Pkd1/Anks3 genetic epistasis in mice, phosphorylation state analysis (preprint)

    PMID:bio_10.1101_2025.04.22.649832

    Open questions at the time
    • Preprint, single lab, not peer-reviewed
    • Kinase/phosphatase controlling polycystin-dependent ANKS3 phosphorylation unidentified
    • Molecular link between ANKS3 and Glis2 regulation undefined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How ANKS3's distinct activities — Bicc1 mRNA condensate control, NPHP/Nek7 interactions, and polycystin-Glis2 signaling — are integrated into one coherent ciliary regulatory program remains unresolved.
  • No unified model linking laterality and renal cyst functions
  • Upstream signals controlling ANKS3 conformation/modification in vivo unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0140313 molecular sequestering activity 2
Localization
GO:0005829 cytosol 2 GO:0005929 cilium 2
Partners
ANKS6BICC1HIF1ANNEK7NPHP1
Complex memberships
ANKS3-ANKS6-Bicc1 giant macromolecular complex

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 polymerizes and ANKS6-SAM binds to one end of the polymer. Crystal structures of the ANKS3-SAM polymer and ANKS3-SAM/ANKS6-SAM complex were determined, revealing molecular details of their association. The disease-associated R823W mutation in ANKS6-SAM dramatically destabilizes the SAM domain, causing loss of interaction with ANKS3-SAM. Crystal structure determination, biochemical binding assays, site-directed mutagenesis BMC structural biology High 24998259
2015 Anks3 interacts with multiple nephronophthisis proteins (NPHPs) as well as Bicc1 and HIF1AN. GFP-tagged Anks3 localizes to the cilium in multi-ciliated epidermal cells. 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 live imaging/localization, zebrafish morpholino knockdown Kidney international Medium 25671767
2015 ANKS3 interacts with the NIMA-related kinase Nek7 through its N-terminal ankyrin repeats, and this interaction results in an ~20 kDa molecular weight modification of Anks3 (not attributable to Nek7-dependent phosphorylation, as a kinase-dead Nek7 mutant also causes the modification). ANKS3 retains Nek7 in the cytoplasm, preventing Nek7 nuclear localization. Co-immunoprecipitation, mass spectrometry (phosphorylation mapping), 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 both proteins co-localize in mouse renal cilia in vivo. Downregulation of Anks3 in vivo in mice altered transcription of vasopressin-induced genes, genes encoding cilium structural proteins, and apoptosis/proliferation genes. Yeast two-hybrid, co-immunoprecipitation, in vivo immunofluorescence/localization in mouse kidney, in vivo LNA antisense oligonucleotide knockdown with transcriptional profiling 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 giant assemblies are shaped by SAM domains, flanking sequences, and SAM-independent protein-protein and protein-mRNA interactions. Crystal structure of Bicc1-SAM polymer, domain-mapping interaction assays with full-length and truncated proteins, in vivo co-localization Structure High 29290488
2016 A homozygous loss-of-function variant in ANKS3 causes laterality defects in humans. Mutant ANKS3 RNA failed to rescue laterality defects in zebrafish anks3 morphants (unlike wild-type RNA), and a new CRISPR/mutant anks3 zebrafish line displays laterality defects in the homozygous state, confirming ANKS3's role in right-left axis determination. Human genetics (autozygome + exome sequencing), zebrafish morpholino rescue assay with wild-type vs. mutant RNA, CRISPR-engineered mutant zebrafish line Human genetics Medium 27417436
2023 ANKS3 has a C-terminal coiled-coil domain that interacts with Bicc1 and inhibits binding of target mRNAs to Bicc1. ANKS6 regulates the conformation of ANKS3, relieving this inhibition. A CRISPR-engineered truncation of ANKS3 leads to symmetric mRNA decay of Dand5 (mediated by Bicc1), demonstrating that ANKS3 conformation controls laterality specification via Bicc1 mRNA binding. AlphaFold structural prediction with biochemical validation, in vitro reconstitution, CRISPR-engineered truncation in animal model PLoS biology Medium 37733651
2023 ANKS3 disperses Bicc1 cytoplasmic granules and concomitantly releases bound mRNAs; co-recruitment of ANKS6 by ANKS3 reinstates Bicc1 condensation and ribonucleoparticle assembly. Bicc1 head-to-tail SAM polymers are interconnected by KH domains to mediate liquid-to-gel phase transitioning of client transcripts, with dual and opposing regulation by ANKS3 and ANKS6. In vitro reconstitution, RNA-binding assays, phase-separation/condensate imaging iScience Medium 37275520
2025 Anks3 acts as a cytosolic regulator of polycystin-dependent cilia signaling: it regulates polycystin-dependent Glis2 expression in vitro and in vivo, undergoes polycystin-dependent changes in phosphorylation state, and functions downstream of cilia and polycystins but upstream of Glis2. Inactivation of Anks3 in Pkd1 mouse models suppresses cyst progression. Translating ribosome affinity purification (TRAP)-RNAseq, in vitro and in vivo genetic inactivation (Pkd1/Anks3 mouse models), phosphorylation state analysis 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 21 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

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