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- EMDB-77058: IST1 bound to PI(4,5)P2 containing membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-77058
TitleIST1 bound to PI(4,5)P2 containing membrane
Map dataSharpenned map
Sample
  • Complex: Regulator of Vps4 activity in the MVB pathway (Ist1)
    • Protein or peptide: IST1 homolog
  • 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
Function / homology
Function and homology information


MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / positive regulation of collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body assembly / Flemming body / endoplasmic reticulum-Golgi intermediate compartment ...MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / positive regulation of collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body assembly / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of proteolysis / establishment of protein localization / azurophil granule lumen / intracellular protein localization / nuclear envelope / protein transport / midbody / cadherin binding / protein domain specific binding / cell division / Neutrophil degranulation / centrosome / chromatin / protein-containing complex binding / extracellular exosome / extracellular region / identical protein binding / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsAlian A / Moss III FR / Talledge N / 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_77058.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.)
0.73 Å/pix.
x 420 pix.
= 306.432 Å		0.73 Å/pix.
x 420 pix.
= 306.432 Å		0.73 Å/pix.
x 420 pix.
= 306.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.7263143 - 5.90567
Average (Standard dev.)0.026469015 (±0.16513337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 306.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77058_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsubtracted map

Fileemd_77058_additional_1.map
AnnotationUnsubtracted map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpenned map

Fileemd_77058_additional_2.map
AnnotationUnsharpenned map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_77058_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_77058_half_map_2.map
AnnotationHalf map 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 : Regulator of Vps4 activity in the MVB pathway (Ist1)

EntireName: Regulator of Vps4 activity in the MVB pathway (Ist1)
Components
  • Complex: Regulator of Vps4 activity in the MVB pathway (Ist1)
    • Protein or peptide: IST1 homolog
  • 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: Regulator of Vps4 activity in the MVB pathway (Ist1)

SupramoleculeName: Regulator of Vps4 activity in the MVB pathway (Ist1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Regulator of Vps4 activity in the MVB pathway.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: IST1 homolog

MacromoleculeName: IST1 homolog / type: protein_or_peptide / ID: 1 / Details: residues 1-2 and 186-364 are unstructured / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.796402 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MLGSGFKAER LRVNLRLVIN RLKLLEKKKT ELAQKARKEI ADYLAAGKDE RARIRVEHII REDYLVEAME ILELYCDLLL ARFGLIQSM KELDSGLAES VSTLIWAAPR LQSEVAELKI VADQLCAKYS KEYGKLCRTN QIGTVNDRLM HKLSVEAPPK I LVERYLIE ...String:
MLGSGFKAER LRVNLRLVIN RLKLLEKKKT ELAQKARKEI ADYLAAGKDE RARIRVEHII REDYLVEAME ILELYCDLLL ARFGLIQSM KELDSGLAES VSTLIWAAPR LQSEVAELKI VADQLCAKYS KEYGKLCRTN QIGTVNDRLM HKLSVEAPPK I LVERYLIE IAKNYNVPYE PDSVVMAEAP PGVETDLIDV GFTDDVKKGG PGRGGSGGFT APVGGPDGTV PMPMPMPMPS AN TPFSYPL PKGPSDFNGL PMGTYQAFPN IHPPQIPATP PSYESVDDIN ADKNISSAQI VGPGPKPEAS AKLPSRPADN YDN FVLPEL PSVPDTLPTA SAGASTSASE DIDFDDLSRR FEELKKKT

UniProtKB: IST1 homolog

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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: 82 / 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 statehelical array

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Sample preparation

BufferpH: 8
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 284 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: TFS FALCON 4i (4k x 4k) / #0 - Digitization - Dimensions - Width: 4096 pixel / #0 - Digitization - Dimensions - Height: 4096 pixel / #0 - Number grids imaged: 1 / #0 - Number real images: 54779 / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2
#1 - Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
#1 - Digitization - Dimensions - Width: 6144 pixel / #1 - Digitization - Dimensions - Height: 4096 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 15877 / #1 - Average electron dose: 45.0 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: 1.3 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Final reconstructionApplied symmetry - Helical parameters - Δz: 3.67 Å
Applied symmetry - Helical parameters - Δ&Phi: -134.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 652823
CTF correctionType: NONE
Segment selectionNumber selected: 3381581 / Software - Name: cryoSPARC (ver. 4.7.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3frr

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3frr


Chain - Residue range: 1-191 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 68.6
Output model

PDB-13gj:
IST1 bound to PI(4,5)P2 containing membrane

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