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- EMDB-77060: CHMP1A bound to PI(4,5)P2 containing membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-77060
TitleCHMP1A bound to PI(4,5)P2 containing membrane
Map dataSharpenned map
Sample
  • Complex: Charged multivesicular body protein 1a
    • Protein or peptide: Charged multivesicular body protein 1a
  • Ligand: [(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
  • Ligand: water
KeywordsESCRT / ESCRT-III / PIP2 / PI(4 / 5)P2 / endosomal / cytokinesis / LIPID BINDING PROTEIN / 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
Charged multivesicular body protein 1a
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAlian A / Talledge N / Moss III FR / McCullough J / Frost A / Sundquist WI
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77060.png

Downloads & links

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Map

FileDownload / File: emd_77060.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpenned map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 576 pix.
= 576. Å		1 Å/pix.
x 576 pix.
= 576. Å		1 Å/pix.
x 576 pix.
= 576. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4748915 - 1.2137275
Average (Standard dev.)0.012019434 (±0.069338106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 576.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77060_msk_1.map
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Additional map: Local refinement sharpenned map

Fileemd_77060_additional_1.map
AnnotationLocal refinement sharpenned map
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Additional map: Unsharpenned map

Fileemd_77060_additional_2.map
AnnotationUnsharpenned map
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Half map: Map half-1

Fileemd_77060_half_map_1.map
AnnotationMap half-1
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Half map: Map half-2

Fileemd_77060_half_map_2.map
AnnotationMap half-2
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Sample components

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Entire : Charged multivesicular body protein 1a

EntireName: Charged multivesicular body protein 1a
Components
  • Complex: Charged multivesicular body protein 1a
    • Protein or peptide: Charged multivesicular body protein 1a
  • Ligand: [(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
  • Ligand: water

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Supramolecule #1: Charged multivesicular body protein 1a

SupramoleculeName: Charged multivesicular body protein 1a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Charged multivesicular body protein 1a
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.70221 kDa/nm

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Macromolecule #1: Charged multivesicular body protein 1a

MacromoleculeName: Charged multivesicular body protein 1a / type: protein_or_peptide / ID: 1 / Details: residues 164-196 are unstructured / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.731812 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MDDTLFQLKF TAKQLEKLAK KAEKDSKAEQ AKVKKALLQK NVECARVYAE NAIRKKNEGV NWLRMASRVD AVASKVQTAV TMKGVTKNM AQVTKALDKA LSTMDLQKVS SVMDRFEQQV QNLDVHTSVM EDSMSSATTL TTPQEQVDSL IMQIAEENGL E VLDQLSQL ...String:
MDDTLFQLKF TAKQLEKLAK KAEKDSKAEQ AKVKKALLQK NVECARVYAE NAIRKKNEGV NWLRMASRVD AVASKVQTAV TMKGVTKNM AQVTKALDKA LSTMDLQKVS SVMDRFEQQV QNLDVHTSVM EDSMSSATTL TTPQEQVDSL IMQIAEENGL E VLDQLSQL PEGASAVGES SVRSQEDQLS RRLAALRN

UniProtKB: Charged multivesicular body protein 1a

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Macromolecule #2: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(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
type: ligand / ID: 2 / Number of copies: 1 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

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

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 284 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 73224 / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsAll images were processed using the same pipeline
Final reconstructionApplied symmetry - Helical parameters - Δz: 1.19 Å
Applied symmetry - Helical parameters - Δ&Phi: 10.948 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.4) / Number images used: 150055
CTF correctionType: NONE
Segment selectionNumber selected: 1050919 / Software - Name: RELION (ver. 5.0-beta)
Startup modelType of model: INSILICO MODEL / In silico model: ModelAngelo and AlphaFold
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: Other, initial_model_type: in silico modelModelAngelo
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 107.8
Output model

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

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