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- PDB-13gm: CHMP1A bound to PI(4,5)P2 containing membrane -

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Basic information

Entry
Database: PDB / ID: 13gm
TitleCHMP1A bound to PI(4,5)P2 containing membrane
ComponentsCharged multivesicular body protein 1a
KeywordsLIPID BINDING PROTEIN / ESCRT / ESCRT-III / PIP2 / PI(4 / 5)P2 / endosomal / cytokinesis / CHMP1A
Function / homology
Function and homology information


multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / nuclear membrane reassembly / multivesicular body sorting pathway ...multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / nuclear membrane reassembly / multivesicular body sorting pathway / midbody abscission / membrane fission / plasma membrane repair / multivesicular body assembly / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / nucleus organization / late endosome to vacuole transport / mitotic chromosome condensation / regulation of mitotic spindle assembly / regulation of centrosome duplication / viral budding via host ESCRT complex / microtubule organizing center / autophagosome membrane / nuclear pore / autophagosome maturation / mitotic metaphase chromosome alignment / multivesicular body / vesicle-mediated transport / endomembrane system / viral budding from plasma membrane / condensed nuclear chromosome / HCMV Late Events / autophagy / kinetochore / nuclear matrix / metallopeptidase activity / protein transport / midbody / early endosome / negative regulation of gene expression / protein domain specific binding / cell division / lysosomal membrane / protein homodimerization activity / DNA-templated transcription / extracellular exosome / nucleoplasm / zinc ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Chem-PIO / Charged multivesicular body protein 1a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAlian, A. / Talledge, N. / Moss III, F.R. / McCullough, J. / Frost, A. / Sundquist, W.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI051174 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Phosphatidylinositol diphosphate binding by ESCRT-III filaments.
Authors: Akram Alian / John McCullough / Frank R Moss / Nathaniel Talledge / Arshad Mohammed / Cecilia D Gerstner / Jacob A Dalluge / Elliott L Paine / Omar Davulcu / Chi-Lun Chang / Adam Frost / Wesley I Sundquist /
Abstract: Different inositol phospholipids (PIPs) distribute to distinct subcellular organelles, creating an addressing system that dictates the sites of action of PIP-binding proteins, including components of ...Different inositol phospholipids (PIPs) distribute to distinct subcellular organelles, creating an addressing system that dictates the sites of action of PIP-binding proteins, including components of the Endosomal Sorting Complexes Required for Transport (ESCRT). The ESCRT machinery is recruited to remodel many different cellular membranes through combinatorial binding interactions made by the early-acting ESCRT-I and ESCRT-II complexes with PIPs, ubiquitin modifications, and membrane-specific adaptors. Membrane remodeling, constriction, and fission are then mediated by membrane-associated filaments formed by subunits of the late-acting ESCRT-III complexes, together with their associated VPS4 AAA ATPases. Here, we describe two different classes of helical ESCRT-III filaments that can surround and tubulate membranes containing PIP lipids. Cryo-EM reconstructions revealed that protofilaments comprising closed IST1 subunits formed 8-stranded nanotubes that encase membrane monolayers. The nanotube coordinates exposed PI(4,5)P or PI(3,5)P headgroups within a basic pocket formed at the junction of three IST1 subunits, and our structures reveal how the pocket can accommodate either PIP isomer with minimal adjustment. In contrast, protofilaments comprising open CHMP1A subunits formed one start helices that encase membrane bilayers and bind exposed PI(4,5)P headgroups across a basic surface that spans adjacent subunits of the CHMP1A protofilament. These two different structures extend the known plasticity of ESCRT-III polymers, reveal how PIP lipids can promote ESCRT-III filament assembly and membrane remodeling, and define the molecular contacts that underlie specific ESCRT-III/PIP interactions.
History
DepositionMay 5, 2026Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Charged multivesicular body protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4782
Polymers21,7321
Non-polymers7471
Water181
1
C: Charged multivesicular body protein 1a
hetero molecules
x 81


Theoretical massNumber of molelcules
Total (without water)1,820,749162
Polymers1,760,27781
Non-polymers60,47281
Water1,45981
TypeNameSymmetry operationNumber
point symmetry operation80
identity operation1_555x,y,z1

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Components

#1: Protein Charged multivesicular body protein 1a / Chromatin-modifying protein 1a / CHMP1a / Vacuolar protein sorting-associated protein 46-1 / Vps46- ...Chromatin-modifying protein 1a / CHMP1a / Vacuolar protein sorting-associated protein 46-1 / Vps46-1 / hVps46-1


Mass: 21731.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 164-196 are unstructured / Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP1A, CHMP1, KIAA0047, PCOLN3, PRSM1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HD42
#2: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Charged multivesicular body protein 1a / Type: COMPLEX / Details: Charged multivesicular body protein 1a / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 21.70221 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 284 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 73224

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Processing

EM software
IDNameVersionCategory
1RELION5.0-betaparticle selection
2SerialEM4.1.0 betaimage acquisition
7ModelAngelo1.0.8model fitting
8UCSF Chimera1.17.3model fitting
12PHENIX2.0-5936model refinement
16cryoSPARC5.0.43D reconstruction
Image processingDetails: All images were processed using the same pipeline
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 10.948 ° / Axial rise/subunit: 1.19 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 1050919
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150055 / Symmetry type: HELICAL
Atomic model buildingB value: 107.8 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model building
ID 3D fitting-IDDetails (eV)Source nameType
11ModelAngeloOtherin silico model
21AlphaFoldin silico model

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