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- PDB-13gh: IST1 bound to PI(3,5)P2 containing membrane -

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Basic information

Entry
Database: PDB / ID: 13gh
TitleIST1 bound to PI(3,5)P2 containing membrane
ComponentsIST1 homolog
KeywordsLIPID BINDING PROTEIN / ESCRT / ESCRT-III / PIP2 / PI(3 / 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-EUJ / IST1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsMoss III, F.R. / Talledge, N. / Alian, A. / 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: 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
C: IST1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3212
Polymers21,5741
Non-polymers7471
Water45025
1
C: IST1 homolog
hetero molecules
x 41


Theoretical massNumber of molelcules
Total (without water)915,15582
Polymers884,54641
Non-polymers30,60941
Water73941
TypeNameSymmetry operationNumber
point symmetry operation40
identity operation1_555x,y,z1

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Components

#1: Protein IST1 homolog / hIST1 / Putative MAPK-activating protein PM28


Mass: 21574.281 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-189)
Source method: isolated from a genetically manipulated source
Details: Residues 1-2 and 189 are unstructured / Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P53990
#2: Chemical ChemComp-EUJ / (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: IST1 homolog / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 7497
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
7UCSF ChimeraX1.10.1model fitting
12RELION4.0.13D reconstruction
13ISOLDE1.10.1model refinement
14PHENIX2.0-5936model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -134.29 ° / Axial rise/subunit: 3.669 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 1532335
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155247 / Symmetry type: HELICAL
Atomic model buildingB value: 93.69 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 3FRR

3frr


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

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