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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 / 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 ...MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / 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 / intracellular protein localization / azurophil granule lumen / nuclear envelope / protein transport / midbody / cadherin binding / protein domain specific binding / cell division / centrosome / Neutrophil degranulation / protein-containing complex binding / chromatin / 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 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_77058.png

Downloads & links

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Map

FileDownload / File: emd_77058.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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

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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

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Additional map: Unsubtracted map

Fileemd_77058_additional_1.map
AnnotationUnsubtracted map
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Additional map: Unsharpenned map

Fileemd_77058_additional_2.map
AnnotationUnsharpenned map
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AxesZYX

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Histogram

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Half map: Half map 1

Fileemd_77058_half_map_1.map
AnnotationHalf map 1
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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_77058_half_map_2.map
AnnotationHalf map 2
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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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