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- PDB-9hhe: Structure of the Ist2 TMEM16 homology domain in the detergent GDN -

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Basic information

Entry
Database: PDB / ID: 9hhe
TitleStructure of the Ist2 TMEM16 homology domain in the detergent GDN
ComponentsIncreased sodium tolerance protein 2
KeywordsMEMBRANE PROTEIN / TMEM16 proteins / lipid scramblase / lipid transport / membrane contact sites / tethering 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: 2.84 Å
AuthorsArndt, M. / Dutzler, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation215236 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
DepositionNov 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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) / 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: Homodimer of N-terminal 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)
Buffer solutionpH: 7.6
SpecimenConc.: 2.56 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 4 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 magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 62.43 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 400925 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingAccession code: AF-P38250-F1-v4 / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049518
ELECTRON MICROSCOPYf_angle_d0.56212936
ELECTRON MICROSCOPYf_dihedral_angle_d3.8351197
ELECTRON MICROSCOPYf_chiral_restr0.0421468
ELECTRON MICROSCOPYf_plane_restr0.0041578

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