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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 / 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
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.USA / Year: 2026
Title: Phosphatidylinositol Diphosphate Binding by ESCRT-III Filaments
Authors: Alian A / McCullough J / Moss III FR / Talledge N / Mohammed A / Gerstner C / Dalluge J / Paine E / Davulcu O / Chang CL / Frost A / Sundquist WI
History
DepositionMay 5, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77060.png

Downloads & links

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Map

FileReleased
AnnotationSharpenned map
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

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
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement sharpenned map

Fileemd_77060_additional_1.map
AnnotationLocal refinement sharpenned map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpenned map

Fileemd_77060_additional_2.map
AnnotationUnsharpenned map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map half-1

Fileemd_77060_half_map_1.map
AnnotationMap half-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map half-2

Fileemd_77060_half_map_2.map
AnnotationMap half-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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