Affinage

IFT54

TRAF3-interacting protein 1 · UniProt Q8TDR0

Length
691 aa
Mass
78.6 kDa
Annotated
2026-04-28
13 papers in source corpus 10 papers cited in narrative 10 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

IFT54 (TRAF3IP1/MIP-T3) is a core subunit of the intraflagellar transport complex B (IFT-B) that coordinates ciliary assembly, motor protein engagement, and microtubule regulation. Its C-terminal coiled-coil domain anchors IFT20, is essential for basal body recruitment and IFT complex incorporation, while its middle region directly binds kinesin-II and IFT dynein subunit D1bLIC to control anterograde and retrograde intraflagellar transport; its N-terminal calponin homology domain binds cytoplasmic microtubules and negatively regulates microtubule stability through MAP4 (PMID:28417161, PMID:33368450, PMID:26487268). Beyond the cilium, IFT54 sequesters TRAF3 on microtubules to suppress innate type I interferon signaling by disrupting TRAF3–VISA–TBK1–IRF3 complex formation, and it associates with IL-13Rα1 to inhibit IL-4/IL-13-induced STAT6 activation (PMID:22079989, PMID:10791955, PMID:12935900). Biallelic mutations in TRAF3IP1 cause nephronophthisis-related ciliopathy with renal cysts and microphthalmia (PMID:26487268).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 2000 High

    The initial discovery that MIP-T3/IFT54 is a microtubule-binding protein that recruits TRAF3 to the cytoskeleton established a link between a cytoskeletal scaffold and TRAF3-dependent signaling.

    Evidence In vitro microtubule cosedimentation, reciprocal co-IP of MIP-T3–TRAF3, and CD40L-induced dissociation in HeLa/293 cells

    PMID:10791955

    Open questions at the time
    • Physiological relevance of TRAF3 sequestration was unknown
    • No connection to cilia had been made
    • Whether MIP-T3 has enzymatic activity was untested
  2. 2003 Medium

    Identification of MIP-T3 as a constitutive IL-13Rα1-binding partner that suppresses STAT6 signaling revealed a second non-ciliary regulatory function for the protein.

    Evidence Yeast tri-hybrid, co-IP, dual luciferase reporter, and EMSA in mammalian cells

    PMID:12935900

    Open questions at the time
    • Mechanism of STAT6 inhibition not defined at the molecular level
    • In vivo relevance in immune cells not tested
    • Single-lab finding without independent replication
  3. 2008 High

    Genetic studies in C. elegans and zebrafish repositioned IFT54 (DYF-11) as an IFT-B complex subunit essential for assembling functional kinesin–IFT particle complexes and for ciliogenesis, establishing its primary ciliary role.

    Evidence C. elegans loss-of-function mutants with IFT fluorescent reporters, live imaging of IFT movement, zebrafish morpholino epistasis with BBS4, MDCK localization

    PMID:18173744 PMID:18369462

    Open questions at the time
    • Domain requirements for IFT complex incorporation were unknown
    • Direct motor-binding regions not mapped
    • Mammalian in vivo loss-of-function phenotype was lacking
  4. 2011 High

    Demonstrating that MIP-T3 suppresses type I IFN production by sequestering TRAF3 away from the VISA–TBK1–IKKε–IRF3 signaling axis resolved the functional consequence of the MIP-T3–TRAF3 interaction first reported in 2000.

    Evidence Overexpression/knockdown with IFN-β and ISRE reporters, co-IP of disrupted TRAF3 signaling complexes, Sendai virus and VSV challenge

    PMID:22079989

    Open questions at the time
    • Whether this innate immune function operates independently of ciliary IFT54 pools is unclear
    • In vivo immune phenotype of IFT54 loss not tested
  5. 2015 High

    Patient mutations in TRAF3IP1 linked IFT54 to nephronophthisis-related ciliopathy and uncovered a non-ciliary function as a negative regulator of microtubule stability via MAP4, explaining epithelial polarity and renal cyst phenotypes.

    Evidence Patient mutation identification, siRNA in renal cells with microtubule/polarity assays, zebrafish pronephric cyst and microphthalmia phenotyping

    PMID:26487268

    Open questions at the time
    • Structural basis of the IFT54–MAP4 interaction not determined
    • Whether MAP4 regulation is conserved across tissues is unknown
  6. 2017 High

    Domain dissection in Chlamydomonas resolved that the C-terminal coiled-coil anchors IFT20 and is essential for basal body recruitment, while the N-terminal CH domain binds tubulin but is dispensable for flagellar assembly, establishing a modular architecture for IFT54.

    Evidence Chlamydomonas ift54 mutant rescue with domain-deletion constructs, IFT live imaging, co-IP, immunofluorescence

    PMID:28417161

    Open questions at the time
    • Structural model of IFT54 within the IFT-B complex not available
    • How IFT54 regulates IFT turnaround at the flagellar tip mechanistically unresolved
  7. 2020 High

    Mapping direct binding of kinesin-II and IFT dynein (D1bLIC) to discrete middle regions of IFT54 established it as a central coordinator of both anterograde and retrograde motor engagement, with conserved interactions in mammalian cells.

    Evidence Chlamydomonas internal-deletion mutagenesis, in vitro pull-downs, in vivo IFT imaging, mammalian co-IP

    PMID:33368450

    Open questions at the time
    • Regulation of motor binding and release (e.g., by phosphorylation or cargo load) is unknown
    • Structural details of the IFT54–motor interfaces not resolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the ciliary and non-ciliary (innate immune, IL-13 signaling, microtubule stability) functions of IFT54 are coordinated in vivo remains unresolved, and no mammalian knockout model has been characterized comprehensively.
  • No conditional knockout mouse phenotyping reported
  • Whether distinct IFT54 pools serve ciliary versus immune functions is untested
  • Post-translational regulation (ubiquitination, phosphorylation) and its impact on function partitioning are poorly understood

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0008092 cytoskeletal protein binding 4 GO:0098772 molecular function regulator activity 3 GO:0060090 molecular adaptor activity 2
Localization
GO:0005856 cytoskeleton 4 GO:0005929 cilium 4 GO:0005815 microtubule organizing center 2 GO:0005829 cytosol 2
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 4 R-HSA-162582 Signal Transduction 2 R-HSA-168256 Immune System 1
Partners
DYNC2LI1HSPA8IFT20IL13RA1KIF3AMAP4TRAF3
Complex memberships
IFT-B complex

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 MIP-T3 (IFT54) binds to Taxol-stabilized microtubules and to tubulin in vitro, and recruits TRAF3 to microtubules when both proteins are overexpressed in HeLa cells. The MIP-T3–TRAF3 interaction requires the coiled-coil TRAF-N domain of TRAF3. Upon CD40 ligand stimulation, TRAF3 is released from the TRAF3·MIP-T3 complex and recruited to the CD40 receptor. In vitro microtubule-binding assay, co-immunoprecipitation, overexpression in HeLa and 293 cells The Journal of biological chemistry High 10791955
2003 MIP-T3 (IFT54) constitutively associates with the IL-13 receptor subunit IL-13Rα1 and suppresses IL-4/IL-13-induced STAT6 phosphorylation, as shown by yeast tri-hybrid, co-immunoprecipitation, dual luciferase assay, and EMSA. Yeast tri-hybrid, co-immunoprecipitation, dual luciferase reporter assay, EMSA FEBS letters Medium 12935900
2008 C. elegans DYF-11 (ortholog of mammalian MIP-T3/IFT54) is an IFT-B subcomplex component essential for assembling functional kinesin motor–IFT particle complexes; loss of DYF-11 causes kinesin-II, IFT-A and IFT-B proteins to fail entry into ciliary axonemes, resulting in compromised ciliary structures. Mammalian MIP-T3 localizes to basal bodies and cilia, and zebrafish mipt3 functions synergistically with BBS4 for gastrulation. C. elegans loss-of-function genetics, fluorescence microscopy of IFT components, zebrafish morpholino knockdown epistasis, subcellular localization in MDCK cells PLoS genetics High 18369462
2008 C. elegans DYF-11 (ortholog of MIP-T3/IFT54) moves anterogradely and retrogradely via IFT in cilia, and its coiled-coil domain is required for proper ciliary localization and ciliogenesis; bbs mutant analysis places DYF-11 in IFT complex B. Mammalian Traf3ip1/MIP-T3 localizes to cilia in MDCK renal epithelial cells. Fluorescent protein tagging and live imaging of IFT movement, C. elegans deletion/domain analysis, MDCK cell localization Genes to cells High 18173744
2010 Proteomic immunoprecipitation-MS identified 34 MIP-T3 (IFT54)-associated proteins in HEK293 cells; actin, HSPA8, and tubulin were confirmed as interaction partners by reciprocal co-IP and colocalization, suggesting roles in cytoskeletal dynamics beyond microtubules. Immunoprecipitation coupled to mass spectrometry, reciprocal co-IP, colocalization microscopy Proteomics Medium 20391533
2011 MIP-T3 (IFT54) is degraded via the ubiquitin-proteasome system in human cell lines, and its C-terminus is required for ubiquitination and proteasome-mediated degradation. Proteasome inhibitor treatment, ubiquitination assays, C-terminal deletion constructs in human cell lines FEBS letters Medium 21510943
2011 MIP-T3 (IFT54) acts as a negative regulator of innate type I IFN production by interacting with TRAF3 and disrupting, in a dose-dependent manner, the formation of TRAF3 complexes with VISA, TBK1, IKKε, and IRF3. MIP-T3 depletion facilitates Sendai virus-induced IFN activation and reduces VSV replication. MIP-T3 dissociates from TRAF3 during viral infection. Overexpression/knockdown, reporter assays (ISRE, IFN-β promoter), co-immunoprecipitation, IRF3 phosphorylation assay, viral challenge Journal of immunology High 22079989
2015 Human IFT54 (TRAF3IP1) is a subunit of the IFT-B complex required for ciliogenesis, and patient mutations reveal it acts as a negative regulator of microtubule stability via MAP4. Loss of IFT54 leads to altered epithelialization/polarity in renal cells and pronephric cysts and microphthalmia in zebrafish. Patient mutation identification, zebrafish knockdown (pronephric cyst/microphthalmia readout), siRNA knockdown in renal cells with microtubule/polarity assays, MAP4 interaction Nature communications High 26487268
2017 In Chlamydomonas, the N-terminal calponin homology (CH) domain of IFT54 interacts with tubulins/microtubules and regulates flagellar import of IFT54 and axonemal association, but is dispensable for flagellar assembly. The C-terminal coiled-coil (CC) domain is essential for binding IFT20, recruitment to the basal body, and incorporation into IFT complexes; complete loss of IFT54 or CC domain destabilizes IFT20. IFT54 also regulates IFT turnaround at the flagellar tip. Chlamydomonas ift54 mutant rescue with domain deletion constructs, IFT imaging, co-immunoprecipitation, immunofluorescence Cellular and molecular life sciences High 28417161
2020 IFT54 directly interacts with kinesin-II and IFT dynein subunit D1bLIC and regulates anterograde IFT. Deletion of residues 342–356 diminishes anterograde IFT traffic and causes accumulation of IFT motors in the proximal cilium with strengthened IFT54–kinesin-II interaction in vitro and in vivo. Deletion of residues 261–275 reduces ciliary entry and anterograde traffic of IFT dynein and reduces IFT54–D1bLIC interaction. These motor interactions are conserved in mammalian cells. Chlamydomonas domain-deletion mutagenesis, in vitro pull-down, in vivo IFT imaging, co-immunoprecipitation in mammalian cells The EMBO journal High 33368450

Source papers

Stage 0 corpus · 13 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2003 DISC1 (Disrupted-In-Schizophrenia 1) is a centrosome-associated protein that interacts with MAP1A, MIPT3, ATF4/5 and NUDEL: regulation and loss of interaction with mutation. Human molecular genetics 314 12812986
2015 Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization. Nature communications 84 26487268
2000 MIP-T3, a novel protein linking tumor necrosis factor receptor-associated factor 3 to the microtubule network. The Journal of biological chemistry 57 10791955
2008 An essential role for DYF-11/MIP-T3 in assembling functional intraflagellar transport complexes. PLoS genetics 48 18369462
2011 MIP-T3 is a negative regulator of innate type I IFN response. Journal of immunology (Baltimore, Md. : 1950) 41 22079989
2008 Caenorhabditis elegans DYF-11, an orthologue of mammalian Traf3ip1/MIP-T3, is required for sensory cilia formation. Genes to cells : devoted to molecular & cellular mechanisms 40 18173744
2017 IFT54 regulates IFT20 stability but is not essential for tubulin transport during ciliogenesis. Cellular and molecular life sciences : CMLS 35 28417161
2020 IFT54 directly interacts with kinesin-II and IFT dynein to regulate anterograde intraflagellar transport. The EMBO journal 33 33368450
2003 MIP-T3 associates with IL-13Ralpha1 and suppresses STAT6 activation in response to IL-13 stimulation. FEBS letters 16 12935900
2010 Proteomic analysis reveals novel binding partners of MIP-T3 in human cells. Proteomics 14 20391533
2022 The MIP-T3 from shrimp Litopenaeus vannamei restricts white spot syndrome virus infection via regulating NF-κB activation. Fish & shellfish immunology 6 35697271
2011 The C-terminus of MIP-T3 protein is required for ubiquitin-proteasome-mediated degradation in human cells. FEBS letters 4 21510943
2020 MIP-T3 Expression Associated with Defects of Ciliogenesis in Airway of COPD Patients. Canadian respiratory journal 2 32104517