Affinage

IFITM3

Interferon-induced transmembrane protein 3 · UniProt Q01628

Length
133 aa
Mass
14.6 kDa
Annotated
2026-06-10
7 papers cited in narrative 8 extracted findings
Cross-family judge vs UniProt: Affinage preferred

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

IFITM3 is an interferon-induced transmembrane protein that restricts entry of enveloped viruses by accumulating in late endosomes and lysosomes, where it raises a barrier to viral membrane fusion [PMID:bio_10.1101_2025.05.27.656272]. Its CD225 domain carries a GxxxG motif that drives multimerization, an activity required to reduce membrane fluidity and to mount antiviral activity against Influenza A virus; the same motif mediates protein-protein interactions including with IFITM1 [PMID:bio_10.1101_2025.06.01.657267]. IFITM3 and IFITM1 co-reside in acidic late endosomal/lysosomal membranes and form a complex, and IFITM3 is sufficient to direct IFITM1 to these endolysosomal/perinuclear compartments, with the two proteins cooperatively and non-redundantly restricting Influenza A entry; loss of functional IFITM3 redistributes IFITM1 to the plasma membrane [PMID:bio_10.1101_2025.06.01.657267, PMID:bio_10.1101_2025.07.16.661931]. A SNARE-like motif within the CD225 domain additionally allows IFITM3 to bind the SNARE fusogen syntaxin 7, disrupting assembly of the SNARE complex that governs homotypic late endosome fusion and accelerating trafficking of endosomal cargo to lysosomes; mutations that abrogate syntaxin 7 binding abolish antiviral activity [PMID:bio_10.1101_2024.08.07.607021]. IFITM3 also restricts HIV-1, an activity counteracted by HIV-1 Nef, which uses the endocytic adaptor AP-2 to redistribute IFITM3, impair its oligomerization, restore membrane fluidity, and reduce its incorporation into virions [PMID:bio_10.1101_2025.05.15.654345]. Pharmacological agents act on this restriction: cyclosporine A sequesters IFITM3 into intraluminal vesicles to permit viral fusion at the limiting membrane [PMID:bio_10.1101_2025.05.27.656272], and a cyclosporine A analogue, BG147, drives lysosomal-dependent IFITM3 mislocalization and degradation to enhance lentiviral transduction [PMID:bio_10.1101_2025.08.26.669098].

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 2024 High

    Established a molecular basis for how IFITM3 interferes with endosomal membrane dynamics, identifying syntaxin 7 as a direct binding partner whose engagement is mechanistically coupled to restriction.

    Evidence Co-immunoprecipitation, in vitro binding, mutagenesis with Influenza A viral readout, and endosomal cargo trafficking assays

    PMID:bio_10.1101_2024.08.07.607021

    Open questions at the time
    • Structural basis of the SNARE-like motif/STX7 interface not resolved
    • Whether STX7 disruption generalizes to restriction of other enveloped viruses untested
    • Preprint, not yet peer-reviewed
  2. 2024 Low

    Extended IFITM3's restriction barrier to SARS-CoV-2, implicating it as an entry barrier overcome by Amphotericin B.

    Evidence siRNA knockdown of IFITM1/2/3 with SARS-CoV-2 entry/replication assay in multiple cell lines

    PMID:bio_10.1101_2024.11.07.622419

    Open questions at the time
    • Indirect inference from combined knockdown; IFITM3-specific contribution not dissected
    • No mechanistic detail of how IFITM3 blocks SARS-CoV-2
    • Preprint, not independently confirmed
  3. 2025 Medium

    Defined the GxxxG motif in the CD225 domain as the structural determinant of IFITM3 multimerization required for reducing membrane fluidity and antiviral activity, linking oligomerization to function.

    Evidence Immunoprecipitation-mass spectrometry, GxxxG mutagenesis, and membrane fluidity assays

    PMID:bio_10.1101_2025.06.01.657267

    Open questions at the time
    • Stoichiometry and architecture of the multimer not determined
    • Direct demonstration that fluidity change blocks fusion not shown
    • Preprint, single lab
  4. 2025 Medium

    Showed IFITM3 acts as an organizer of IFITM family localization, directing IFITM1 to endolysosomes for cooperative, non-redundant restriction.

    Evidence Co-IP, proximity ligation, siRNA knockdown, knockout/rescue co-expression, and immunofluorescence localization across two studies

    PMID:bio_10.1101_2025.06.01.657267 PMID:bio_10.1101_2025.07.16.661931

    Open questions at the time
    • Mechanism by which IFITM3 retains IFITM1 in endolysosomes not defined
    • Whether the IFITM1-IFITM3 complex is direct or bridged not resolved
    • Preprint
  5. 2025 Medium

    Revealed a viral antagonism mechanism, showing HIV-1 Nef counteracts IFITM3 via AP-2-dependent redistribution and impaired oligomerization.

    Evidence Co-IP, flow cytometry for surface levels, virion incorporation, oligomerization and membrane fluidity assays, siRNA knockdown

    PMID:bio_10.1101_2025.05.15.654345

    Open questions at the time
    • Direct Nef-IFITM3 binding interface not mapped
    • Clade-dependence mechanism not fully explained
    • Preprint, single lab
  6. 2025 Medium

    Demonstrated that IFITM3 restriction is pharmacologically tractable, with cyclosporine A and an analogue redistributing or degrading IFITM3 to relieve the fusion block.

    Evidence Differential permeabilization immunostaining, super-resolution microscopy, BG147 treatment with lysosomal inhibitors, and lentiviral transduction assays in vivo and ex vivo

    PMID:bio_10.1101_2025.05.27.656272 PMID:bio_10.1101_2025.08.26.669098

    Open questions at the time
    • Molecular target through which CsA/BG147 acts on IFITM3 not identified
    • Whether sequestration and degradation share a common pathway unclear
    • Preprint

Open questions

Synthesis pass · forward-looking unresolved questions
  • How IFITM3 multimerization, SNARE engagement, and membrane fluidity changes are integrated into a single fusion-blocking mechanism, and the structural basis of these activities, remain unresolved.
  • No high-resolution structure of IFITM3 or its complexes
  • Quantitative relationship between fluidity, oligomer state, and fusion arrest undefined
  • Generality across the full range of restricted enveloped viruses untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140313 molecular sequestering activity 2 GO:0098772 molecular function regulator activity 1
Localization
GO:0005764 lysosome 2 GO:0005768 endosome 2 GO:0005886 plasma membrane 2
Pathway
R-HSA-168256 Immune System 3 R-HSA-5653656 Vesicle-mediated transport 1
Partners
IFITM1STX7

Evidence

Reading pass · 8 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2025 IFITM3 contains a GxxxG motif in its CD225 domain that mediates its multimerization, which is essential for reducing membrane fluidity and for antiviral activity against Influenza A virus. The GxxxG motif also mediates interaction of IFITM3 with other proteins, including IFITM1, as determined by immunoprecipitation coupled with mass spectrometry. Immunoprecipitation coupled with mass spectrometry; mutagenesis of GxxxG motif; membrane fluidity assays bioRxivpreprint Medium bio_10.1101_2025.06.01.657267
2025 Endogenous IFITM1 and IFITM3 co-reside in membranes of acidic late endosomes and lysosomes and form a protein-protein complex, as determined by co-immunoprecipitation and proximity ligation assay. IFITM3 promotes IFITM1 localization to endolysosomes; knockdown of IFITM3 results in enhanced localization of IFITM1 at the plasma membrane. IFITM1 and IFITM3 cooperatively restrict Influenza A virus entry at endolysosomal membranes in a non-redundant manner. Co-immunoprecipitation; proximity ligation assay; siRNA knockdown; hemagglutinin-mediated viral entry assay bioRxivpreprint Medium bio_10.1101_2025.06.01.657267
2024 The CD225 domain of IFITM3 contains a SNARE-like motif that enables interaction with cellular SNARE fusogens. IFITM3 binds to syntaxin 7 (STX7) both in cells and in vitro. Mutations that abrogate STX7 binding cause loss of antiviral activity against Influenza A virus. Mechanistically, IFITM3 disrupts assembly of the SNARE complex controlling homotypic late endosome fusion and accelerates trafficking of endosomal cargo to lysosomes. Co-immunoprecipitation; in vitro binding assay; site-directed mutagenesis; viral infection assay; endosomal cargo trafficking assay bioRxivpreprint High bio_10.1101_2024.08.07.607021
2025 HIV-1 Nef protein (particularly from primary isolates, especially clade C) counteracts IFITM3-mediated restriction of HIV-1 infectivity. Nef interacts with IFITM3 in membranes using the endocytic adaptor AP-2, reduces IFITM3 cell surface levels, increases IFITM3 levels in early endosomes, reduces IFITM3 incorporation into HIV-1 virions, impairs IFITM3 oligomerization, and restores membrane fluidity in IFITM3-expressing cells. Co-immunoprecipitation; flow cytometry for surface levels; virion incorporation assay; membrane fluidity assay; IFITM3 oligomerization assay; siRNA knockdown bioRxivpreprint Medium bio_10.1101_2025.05.15.654345
2025 IFITM3 accumulates in late endosomes where it prevents viral fusion. Cyclosporine A (CsA) treatment causes IFITM3 to be sequestered into intraluminal vesicles (ILVs) of late endosomes, thereby enabling viral fusion with the limiting membrane of these compartments. This redistribution was demonstrated by differential antibody access to the cytoplasmic N-terminus vs. extracellular C-terminus after CsA treatment, and confirmed by super-resolution microscopy showing IFITM3 redistribution from the periphery to the interior of late endosomes. Immunostaining with differential permeabilization protocols (digitonin vs. harsher agents); super-resolution microscopy; antibody accessibility assay bioRxivpreprint Medium bio_10.1101_2025.05.27.656272
2025 A novel cyclosporine A analogue, BG147, causes IFITM proteins (including IFITM3) to be mislocalized and degraded through lysosomal acidification-dependent pathways. This degradation of IFITM3 enhances lentiviral vector transduction ex vivo in hematopoietic stem and progenitor cells and in vivo in mouse photoreceptors. IFITM3 levels functionally return 96 hours after BG147 washout. BG147 pharmacological treatment; immunostaining for IFITM localization; lentiviral transduction assay ex vivo and in vivo; lysosomal inhibitor experiments; washout recovery assay bioRxivpreprint Medium bio_10.1101_2025.08.26.669098
2025 IFITM3 is sufficient to localize IFITM1 to vesicle structures in the perinuclear space. Loss of functional IFITM3 results in a shift of IFITM1 distribution to a predominantly membrane location. In contrast, IFITM3 localization is unaffected by loss of IFITM1. Mutant forms of IFITM3 lead to retention of IFITM1 primarily at the plasma membrane. IFITM3 knockout cell lines (double knockout GSCs); transient expression/co-expression of IFITM1 and IFITM3; immunofluorescence localization; mutagenesis of IFITM3 bioRxivpreprint Medium bio_10.1101_2025.07.16.661931
2024 Knockdown of IFITM3 (and IFITM1/2) suggests that Amphotericin B enhances SARS-CoV-2 cell entry by overcoming the antiviral effect of IFITM3 protein, implicating IFITM3 as a barrier to SARS-CoV-2 entry. siRNA knockdown of IFITM1, 2, and 3; viral entry/replication assay with SARS-CoV-2 in multiple cell lines bioRxivpreprint Low bio_10.1101_2024.11.07.622419

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