Affinage

CHMP3

Charged multivesicular body protein 3 · UniProt Q9Y3E7

Length
222 aa
Mass
25.1 kDa
Annotated
2026-06-09
12 papers in source corpus 8 papers cited in narrative 8 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CHMP3 (VPS24) is an ESCRT-III subunit that drives membrane scission during budding and abscission events by polymerizing into membrane-associated lattices and recruiting downstream remodeling machinery (PMID:16740483, PMID:36604498). Its crystal structure reveals a flat helical fold that assembles into a lattice through two distinct dimerization modes, presenting a highly basic surface for membrane interaction on one face and a C-terminal VPS4-target sequence on the opposite face; mutation of the basic and dimerization regions abolishes bilayer binding and reverses the dominant-negative block of HIV-1 budding (PMID:16740483). In solution CHMP3 toggles between a closed, autoinhibited cytosolic form, in which helix α5 docks onto the tips of helices α1/α2, and an open activated form competent for membrane assembly (PMID:18395747, PMID:21220121). On negatively curved membranes, the open conformer co-polymerizes with CHMP2A into helical heterodimeric filaments whose short N-terminal motifs contact the bilayer and whose C-terminal VPS4-target sequences face the tube interior; electrostatic inter-filament contacts permit VPS4 to constrict and cleave the tubes, defining CHMP2A–CHMP3–VPS4 as a minimal membrane fission machinery (PMID:36604498). CHMP3 additionally recruits the deubiquitylase AMSH via a high-affinity, novel MIM–MIT interaction in which its disordered C-terminal region folds into a helix upon binding the AMSH N-terminal MIT domain (PMID:18395747, PMID:21827950). During cytokinetic abscission CHMP3 acts downstream of CHMP2A in the ordered hierarchical assembly of ESCRT-III [PMID:bio_10.1101_2025.06.24.661003]. A homozygous CHMP3 missense variant causes complex hereditary spastic paraplegia, with loss of CHMP3 function disrupting endosomal and autophagic flux (PMID:35710109); CHMP3 depletion also activates caspase-1-dependent pyroptosis (PMID:38038147).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2006 High

    Established the structural basis for how CHMP3 engages membranes, showing that lattice polymerization with a basic membrane-binding face and an opposed VPS4-target face underlies its role in the final steps of budding.

    Evidence X-ray crystallography at 2.8 Å with site-directed mutagenesis, in vivo membrane interaction assays, and an HIV-1 budding assay

    PMID:16740483

    Open questions at the time
    • Did not resolve how polymerization is triggered on membranes in cells
    • No structure of CHMP3 in complex with partner ESCRT-III subunits
  2. 2008 High

    Resolved that CHMP3 exists in distinct closed (autoinhibited) and open (activated) conformations and that both bind AMSH with high affinity through its C-terminal region plus additional contributing regions.

    Evidence SAXS conformational analysis with ITC binding affinity measurements

    PMID:18395747

    Open questions at the time
    • Did not define the atomic interface of the CHMP3–AMSH contact
    • The trigger converting closed to open state in vivo unresolved
  3. 2011 High

    Defined the CHMP3–AMSH interaction at atomic resolution, revealing a novel MIM that folds upon binding the AMSH MIT domain, distinct from the CHMP1 site, and showed the AMSH N-terminal helix is functionally required for HIV-1 budding.

    Evidence Crystal structure of the AMSHΔC–CHMP3ΔN complex with ITC, SPR, and HIV-1 budding functional assay

    PMID:21827950

    Open questions at the time
    • Functional consequence of CHMP3-recruited AMSH deubiquitylation on cargo not dissected
    • Did not test the MIM–MIT interaction in cytokinesis or endosomal contexts
  4. 2011 Medium

    Refined the molecular architecture of the autoinhibited CHMP3 state, localizing helix α5 against the α1/α2 tips while helix α6 remains free, clarifying which elements gate activation.

    Evidence SAXS ensemble refinement with coarse-grained molecular simulations using a maximum-entropy approach

    PMID:21220121

    Open questions at the time
    • Computational model without mutagenesis validation
    • Did not capture the activation transition directly
  5. 2022 Medium

    Linked CHMP3 function to human disease and to endosomal/autophagic flux, showing a missense variant causes hereditary spastic paraplegia with accumulation of endosomes and autophagosomes reversible by wild-type re-expression.

    Evidence Exome sequencing, electron microscopy, western blot, immunofluorescence, and ectopic wild-type rescue in patient fibroblasts

    PMID:35710109

    Open questions at the time
    • Mechanism by which p.Thr173Ile impairs ESCRT-III assembly not defined
    • Single family / single lab
    • Connection between the autophagy defect and neuronal phenotype unestablished
  6. 2023 High

    Captured the active membrane-bound state, showing CHMP2A–CHMP3 heterodimers build open-conformation helical filaments that VPS4 constricts and cleaves, defining a minimal fission machinery.

    Evidence Cryo-EM at 3.3 and 3.6 Å, high-speed AFM, fluorescence microscopy, and in vitro membrane tube reconstitution

    PMID:36604498

    Open questions at the time
    • How additional ESCRT-III subunits modify this minimal filament in vivo unresolved
    • Does not address regulation of filament nucleation
  7. 2023 Medium

    Placed CHMP3 as a suppressor of caspase-1-dependent pyroptosis in hepatocellular carcinoma cells, connecting its loss to membrane integrity failure.

    Evidence siRNA knockdown, western blot of caspase-1 pathway proteins, electron microscopy, caspase-1 inhibitor rescue, and xenograft model

    PMID:38038147

    Open questions at the time
    • Molecular link between ESCRT-III fission activity and caspase-1 activation not defined
    • Single lab / single cancer context
  8. 2025 Medium

    Ordered ESCRT-III assembly during cytokinetic abscission by showing CHMP3 recruitment depends on CHMP2A, placing it downstream in the hierarchy.

    Evidence CHMP2A knockout with live-cell imaging, SIM, and CLEM in mammalian cells (preprint)

    PMID:bio_10.1101_2025.06.24.661003

    Open questions at the time
    • Preprint not yet peer-reviewed
    • Does not establish direct CHMP2A–CHMP3 contact at the abscission site in vivo
    • Timing relative to VPS4 recruitment unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How CHMP3 conformational activation, partner selection (CHMP2A vs AMSH), and disease-associated dysfunction are coordinated within specific cellular fission events remains open.
  • No structure of full ordered ESCRT-III assembly including CHMP3 in a cellular context
  • Mechanistic chain from CHMP3 loss to pyroptosis and to neurodegeneration undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2 GO:0008289 lipid binding 2 GO:0060090 molecular adaptor activity 2
Localization
GO:0005829 cytosol 2 GO:0005886 plasma membrane 2 GO:0005768 endosome 1
Pathway
R-HSA-5653656 Vesicle-mediated transport 2 R-HSA-1640170 Cell Cycle 1 R-HSA-5357801 Programmed Cell Death 1 R-HSA-9612973 Autophagy 1
Partners
AMSHCHMP2AVPS4
Complex memberships
CHMP2A-CHMP3 filamentESCRT-III

Evidence

Reading pass · 8 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2006 Crystal structure of human CHMP3 at 2.8 Å resolution reveals a flat helical arrangement that assembles into a lattice via two distinct dimerization modes, with a highly basic surface that mediates membrane interaction on one side and the C-terminal Vps4-target sequence on the opposite side. Mutations in basic and dimerization regions abolish bilayer interaction in vivo and reverse the dominant-negative effect of truncated CHMP3 on HIV-1 budding, demonstrating that CHMP3 polymerization and lattice formation on membranes underlies its role in the final steps of budding. X-ray crystallography (2.8 Å), site-directed mutagenesis, in vivo membrane interaction assays, HIV-1 budding assay Developmental Cell High 16740483
2008 SAXS data reveal that CHMP3 can adopt two conformations in solution: a closed globular (autoinhibited, cytosolic) form and an open extended (activated) form. Both conformations interact with AMSH with high affinity; the C-terminal region of CHMP3 is required for AMSH interaction, but a C-terminal peptide alone shows only weak binding, indicating additional regions of CHMP3 contribute to the high-affinity interaction. Small-angle X-ray scattering (SAXS), isothermal titration calorimetry (ITC), binding affinity measurements Journal of Molecular Biology High 18395747
2011 Crystal structure of the AMSH N-terminal fragment (AMSHΔC) in complex with the C-terminal region of CHMP3 (CHMP3ΔN) reveals that CHMP3ΔN is disordered in solution but adopts a helical conformation upon binding AMSH, forming a novel MIT-domain interacting motif (MIM) distinct from the CHMP1–AMSH binding site. ITC and SPR measurements confirm an unusually high-affinity MIM–MIT interaction. The N-terminal helical segment of AMSH regulates its function; its destabilization causes loss of function during HIV-1 budding. X-ray crystallography, ITC, SPR, HIV-1 budding functional assay Structure High 21827950
2011 SAXS ensemble refinement using maximum-entropy combination with coarse-grained simulations characterizes the autoinhibited (low-salt) state of CHMP3: helix α5 is bound to the tip of helices α1 and α2, while helix α6 remains free in solution and is not part of the autoinhibitory complex. SAXS ensemble refinement, coarse-grained molecular simulations, maximum-entropy approach Structure Medium 21220121
2023 Cryo-EM structures at 3.3 and 3.6 Å of membrane-coated CHMP2A–CHMP3 filaments show helical filaments assembled by CHMP2A–CHMP3 heterodimers in the open ESCRT-III conformation, generating a partially positive-charged membrane-interaction surface with short N-terminal motifs contacting the membrane and the C-terminal VPS4-target sequence oriented toward the tube interior. Inter-filament interactions are electrostatic, facilitating filament sliding during VPS4-mediated remodeling. High-speed AFM and fluorescence microscopy confirm that VPS4 can constrict and cleave CHMP2A–CHMP3 membrane tubes, establishing CHMP2A–CHMP3–VPS4 as a minimal membrane fission machinery. Cryo-EM (3.3 and 3.6 Å), high-speed atomic force microscopy (HS-AFM), fluorescence microscopy, in vitro membrane tube reconstitution Nature Structural & Molecular Biology High 36604498
2022 A homozygous missense variant in CHMP3 (p.Thr173Ile) causes complex hereditary spastic paraplegia. Patient fibroblasts with reduced CHMP3 levels show accumulation of endosomes, autophagosomes, and autolysosomes by electron microscopy, and elevated autophagy markers p62 and LC3-II. Ectopic re-expression of wild-type CHMP3 in patient fibroblasts reduces p62 puncta and the number of endosomes and autophagosomes, directly linking CHMP3 to regulation of the autophagy/endosomal pathway. Exome sequencing, electron microscopy, western blot, immunofluorescence, ectopic wild-type rescue in primary patient fibroblasts Journal of Medical Genetics Medium 35710109
2023 Knockdown of CHMP3 in hepatocellular carcinoma cells activates the caspase-1 pyroptosis signaling pathway, resulting in changes in cell membrane integrity and cytoplasmic leakage; this effect is reversed by the caspase-1 inhibitor AYC, indicating CHMP3 suppresses caspase-1-dependent pyroptosis. siRNA knockdown, western blot of caspase-1 pathway proteins, transmission electron microscopy, caspase-1 inhibitor rescue, xenograft tumor model International Journal of Oncology Medium 38038147
2025 During mammalian cytokinetic abscission, depletion of CHMP2A causes severe mislocalization of CHMP3 (as well as CHMP4B and CHMP1B) at the abscission site, while IST1 and CHMP2B are minimally affected, placing CHMP3 downstream of CHMP2A in an ordered, hierarchical assembly of ESCRT-III subunits required for timely abscission. CHMP2A knockout, live cell imaging, structured illumination microscopy (SIM), correlative light-electron microscopy (CLEM), dual-protein imaging bioRxiv (preprint)preprint Medium bio_10.1101_2025.06.24.661003

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2011 SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure (London, England : 1993) 209 21220121
2006 Structural basis for budding by the ESCRT-III factor CHMP3. Developmental cell 209 16740483
2008 Structural basis for autoinhibition of ESCRT-III CHMP3. Journal of molecular biology 113 18395747
2023 Structural basis of CHMP2A-CHMP3 ESCRT-III polymer assembly and membrane cleavage. Nature structural & molecular biology 50 36604498
2008 Physiological involvement in pH signaling of Vps24-mediated recruitment of Aspergillus PalB cysteine protease to ESCRT-III. The Journal of biological chemistry 50 19056728
2011 Structural basis for ESCRT-III CHMP3 recruitment of AMSH. Structure (London, England : 1993) 42 21827950
2021 Design principles of the ESCRT-III Vps24-Vps2 module. eLife 19 34028356
2007 Characterization of a novel alternatively spliced human transcript encoding an N-terminally truncated Vps24 protein that suppresses the effects of Bax in an ESCRT independent manner in yeast. Gene 18 17331679
2023 CHMP3 promotes the progression of hepatocellular carcinoma by inhibiting caspase‑1‑dependent pyroptosis. International journal of oncology 16 38038147
2006 Aovps24, a homologue of VPS24, is required for vacuolar formation which could maintain proper growth and development in the filamentous fungus Aspergillus oryzae. Biochemical and biophysical research communications 12 16857172
2022 A homozygous variant in CHMP3 is associated with complex hereditary spastic paraplegia. Journal of medical genetics 7 35710109
2021 Genetic analysis of the Drosophila ESCRT-III complex protein, VPS24, reveals a novel function in lysosome homeostasis. PloS one 4 33956855

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