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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 / 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
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.USA / Year: 2026
Title: Phosphatidylinositol Diphosphate Binding by ESCRT-III Filaments
Authors: Alian, A. / McCullough, J. / Moss III, F.R. / Talledge, N. / Mohammed, A. / Gerstner, C. / Dalluge, J. / Paine, E. / Davulcu, O. / Chang, C.L. / Frost, A. / Sundquist, W.I.
History
DepositionMay 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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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