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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 / regulation of centrosome duplication / membrane fission / late endosome to vacuole transport / multivesicular body assembly / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / mitotic chromosome condensation / plasma membrane repair / regulation of mitotic spindle assembly / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / microtubule organizing center / autophagosome membrane / autophagosome maturation / nuclear pore / multivesicular body / vesicle-mediated transport / endomembrane system / viral budding from plasma membrane / condensed nuclear chromosome / HCMV Late Events / kinetochore / autophagy / nuclear matrix / metallopeptidase activity / protein transport / midbody / early endosome / protein domain specific binding / negative regulation of gene expression / cell division / lysosomal membrane / DNA-templated transcription / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / 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.USA / Year: 2026
Title: Phosphatidylinositol Diphosphate Binding by ESCRT-III Filaments
Authors: Alian, A. / McCullough, J. / Moss III, F.R. / Talledge, N. / Mohammed, A. / Gerstner, C. / Dalluge, J. / Paine, E. / Davulcu, O. / Chang, C.L. / Frost, A. / Sundquist, W.I.
History
DepositionMay 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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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