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- PDB-9qju: Structure of the transmembrane domain of Ist2 in lipid nanodiscs ... -

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Basic information

Entry
Database: PDB / ID: 9qju
TitleStructure of the transmembrane domain of Ist2 in lipid nanodiscs (narrow state)
ComponentsIncreased sodium tolerance protein 2
KeywordsMEMBRANE PROTEIN / lipid Transport / membrane contact sites / scramblase / TMEM16 protein
Function / homology
Function and homology information


Stimuli-sensing channels / cellular bud membrane / endoplasmic reticulum membrane organization / regulation of phosphatidylinositol dephosphorylation / cortical endoplasmic reticulum / chloride channel activity / Neutrophil degranulation / chloride transmembrane transport / cell periphery / protein localization to plasma membrane ...Stimuli-sensing channels / cellular bud membrane / endoplasmic reticulum membrane organization / regulation of phosphatidylinositol dephosphorylation / cortical endoplasmic reticulum / chloride channel activity / Neutrophil degranulation / chloride transmembrane transport / cell periphery / protein localization to plasma membrane / lipid binding / plasma membrane
Similarity search - Function
Anoctamin / : / Calcium-activated chloride channel
Similarity search - Domain/homology
Increased sodium tolerance protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsArndt, M. / Dutzler, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_215236 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for lipid transport at membrane contact sites by the IST2-OSH6 complex.
Authors: Melanie Arndt / Angela Schweri / Raimund Dutzler /
Abstract: Membrane contact sites are hubs for interorganellar lipid transport within eukaryotic cells. As a principal tether bridging the endoplasmic reticulum (ER) and the plasma membrane in Saccharomyces ...Membrane contact sites are hubs for interorganellar lipid transport within eukaryotic cells. As a principal tether bridging the endoplasmic reticulum (ER) and the plasma membrane in Saccharomyces cerevisiae, the protein IST2 has a major role during lipid transport between both compartments. Here, we show a comprehensive investigation elucidating the structural and mechanistic properties of IST2 and its interaction with the soluble lipid transfer protein OSH6. The ER-embedded transmembrane domain of IST2 is homologous to the TMEM16 family and acts as a constitutively active lipid scramblase. The extended C terminus binds to the plasma membrane and the phosphatidylserine-phosphatidylinositol 4-phosphate exchanger OSH6. Through cellular growth assays and biochemical and structural studies, we characterized the interaction between both proteins and show that OSH6 remains associated with IST2 during lipid shuttling between membranes. These results highlight the role of the IST2-OSH6 complex in lipid trafficking and offer initial insights into the relevance of scramblases for carrier-like lipid transport mechanisms.
History
DepositionMar 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Increased sodium tolerance protein 2
A: Increased sodium tolerance protein 2


Theoretical massNumber of molelcules
Total (without water)175,5552
Polymers175,5552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Increased sodium tolerance protein 2


Mass: 87777.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IST2, YBR086C, YBR0809 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): FGY217 / References: UniProt: P38250
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homodimeric transmembrane domain of Ist2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: FGY217
Buffer solutionpH: 7.6
SpecimenConc.: 1.09 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample yielded two reconstructions differing mainly in the size of the nanodisc, which were deposited independently to the PDB.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 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: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 62.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
9PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189991 / Symmetry type: POINT
Atomic model buildingPDB-ID: 9HHE

9hhe


Accession code: 9HHE / Details: high-resultion structure Ist2 1-716 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.34 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028392
ELECTRON MICROSCOPYf_angle_d0.48611406
ELECTRON MICROSCOPYf_dihedral_angle_d5.8221064
ELECTRON MICROSCOPYf_chiral_restr0.041304
ELECTRON MICROSCOPYf_plane_restr0.0041374

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