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- EMDB-53211: Structure of the transmembrane domain of Ist2 in lipid nanodiscs ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53211
TitleStructure of the transmembrane domain of Ist2 in lipid nanodiscs (narrow state)
Map data
Sample
  • Complex: Homodimeric transmembrane domain of Ist2
    • Protein or peptide: Increased sodium tolerance protein 2
Keywordslipid Transport / membrane contact sites / scramblase / TMEM16 protein / MEMBRANE 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsArndt M / Dutzler R
Funding support Switzerland, 1 items
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, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53211.png

Downloads & links

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Map

FileDownload / File: emd_53211.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 240 pix.
= 312.48 Å		1.3 Å/pix.
x 240 pix.
= 312.48 Å		1.3 Å/pix.
x 240 pix.
= 312.48 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.0016632241 - 1.9270942
Average (Standard dev.)0.0007501231 (±0.01982187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 312.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53211_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53211_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Homodimeric transmembrane domain of Ist2

EntireName: Homodimeric transmembrane domain of Ist2
Components
  • Complex: Homodimeric transmembrane domain of Ist2
    • Protein or peptide: Increased sodium tolerance protein 2

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Supramolecule #1: Homodimeric transmembrane domain of Ist2

SupramoleculeName: Homodimeric transmembrane domain of Ist2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Increased sodium tolerance protein 2

MacromoleculeName: Increased sodium tolerance protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 87.777375 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPEQ KLISEEDLGT LEVLFQGPSS QTITSLDPNC VIVFNKTSSA NEKSLNVEF KRLNIHSIIE PGHDLQTSYA FIRIHQDNAK PLFSFLQNLD FIESIIPYHD TELSDDLHKL ISISKSKILE A PKQYELYN ...String:
MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPEQ KLISEEDLGT LEVLFQGPSS QTITSLDPNC VIVFNKTSSA NEKSLNVEF KRLNIHSIIE PGHDLQTSYA FIRIHQDNAK PLFSFLQNLD FIESIIPYHD TELSDDLHKL ISISKSKILE A PKQYELYN LSNLTNNPKQ SLYFAFLQNY IKWLIPFSFF GLSIRFLSNF TYEFNSTYSL FAILWTLSFT AFWLYKYEPF WS DRLSKYS SFSTIEFLQD KQKAQKKASS VIMLKKCCFI PVALLFGAIL LSFQLYCFAL EIFIKQIYNG PMISILSFLP TIL ICTFTP VLTVIYNKYF VEPMTKWENH SSVVNAKKSK EAKNFVIIFL SSYVPLLITL FLYLPMGHLL TAEIRTKVFN AFSI LARLP THDSDFIIDT KRYEDQFFYF IVINQLIQFS MENFVPSLVS IAQQKINGPN PNFVKAESEI GKAQLSSSDM KIWSK VKSY QTDPWGATFD LDANFKKLLL QFGYLVMFST IWPLAPFICL IVNLIVYQVD LRKAVLYSKP EYFPFPIYDK PSSVSN TQK LTVGLWNSVL VMFSILGCVI TATLTYMYQS CNIPGVGAHT SIHTNKAWYL ANPINHSWIN IVLYAVFIEH VSVAIFF LF SSILKSSHDD VANGIVPKHV VNVQNPPKQE VFEKIPSPEF NSNNEKELVQ RKGSANEKLH QELGEKQPAS SANGYEAH A ATHANNDPSS LSSASSPSLS SSSSSSKTGV VKAVDNDTAG SAGKKPLATE STEA

UniProtKB: Increased sodium tolerance protein 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.09 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample yielded two reconstructions differing mainly in the size of the nanodisc, which were deposited independently to the PDB.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 189991
Initial angle assignmentType: OTHER / Details: CryoSPARC
Final angle assignmentType: OTHER / Details: CryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9hhe


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: high-resultion structure Ist2 1-716
Output model

PDB-9qju:
Structure of the transmembrane domain of Ist2 in lipid nanodiscs (narrow state)

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