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

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Basic information

Entry
Database: PDB / ID: 13gj
TitleIST1 bound to PI(4,5)P2 containing membrane
ComponentsIST1 homolog
KeywordsLIPID BINDING PROTEIN / ESCRT / ESCRT-III / PIP2 / PI(4 / 5)P2 / endosomal / cytokinesis
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
Chem-PIO / IST1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2 Å
AuthorsAlian, A. / Moss III, F.R. / Talledge, N. / 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 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, 2026Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IST1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5432
Polymers39,7961
Non-polymers7471
Water1,47782
1
A: IST1 homolog
hetero molecules
x 41


Theoretical massNumber of molelcules
Total (without water)1,662,26282
Polymers1,631,65241
Non-polymers30,60941
Water73941
TypeNameSymmetry operationNumber
point symmetry operation40
identity operation1_555x,y,z1

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Components

#1: Protein IST1 homolog


Mass: 39796.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-2 and 186-364 are unstructured / Source: (gene. exp.) Homo sapiens (human) / Gene: IST1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P53990
#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: isolated from a natural source / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Regulator of Vps4 activity in the MVB pathway (Ist1) / Type: COMPLEX / Details: Regulator of Vps4 activity in the MVB pathway. / Entity ID: #1 / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
1139.97883 kDa/nmYES
21NO
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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
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 magnification: 165000 X / Nominal defocus max: 1300 nm / Nominal defocus min: 400 nm / C2 aperture diameter: 50 µm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector modelNum. of grids imagedNum. of real images
1140TFS FALCON 4i (4k x 4k)154779
2145GATAN K3 BIOCONTINUUM (6k x 4k)115877
Image scans
WidthHeightIDImage recording-IDEntry-ID
409640961113GJ
614440962213GJ

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2SerialEM4.1.0 betaimage acquisition
3EPUimage acquisition
8UCSF Chimeramodel fitting
13cryoSPARC4.7.13D reconstruction
14PHENIX2.0-5936model refinement
CTF correctionType: NONE
Helical symmerty
IDImage processing-IDAngular rotation/subunit (°)Axial rise/subunit (Å)Axial symmetry
11-134.33.67C1
21-134.33.67C1
Particle selectionNum. of particles selected: 3381581
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 652823 / Symmetry type: HELICAL
Atomic model buildingB value: 68.6 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 3FRR

3frr


Accession code: 3FRR / Chain residue range: 1-191 / Pdb chain residue range: 1-191 / Source name: PDB / Type: experimental model

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