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- PDB-9hdk: Structure of s.c.Osh6 in complex with Ist2 732-756 and POPS -

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Basic information

Entry
Database: PDB / ID: 9hdk
TitleStructure of s.c.Osh6 in complex with Ist2 732-756 and POPS
Components
  • Increased sodium tolerance protein 2
  • Oxysterol-binding protein homolog 6
KeywordsLIPID TRANSPORT / Lipid transport protein / complex / Oxysterol-binding protein / membrane contact sites
Function / homology
Function and homology information


Stimuli-sensing channels / cellular bud membrane / Acyl chain remodelling of PS / endoplasmic reticulum membrane organization / regulation of phosphatidylinositol dephosphorylation / sterol transfer activity / sterol homeostasis / sterol binding / phospholipid transporter activity / sterol transport ...Stimuli-sensing channels / cellular bud membrane / Acyl chain remodelling of PS / endoplasmic reticulum membrane organization / regulation of phosphatidylinositol dephosphorylation / sterol transfer activity / sterol homeostasis / sterol binding / phospholipid transporter activity / sterol transport / phosphatidylinositol-5-phosphate binding / cortical endoplasmic reticulum / sterol metabolic process / maintenance of cell polarity / phospholipid transport / phosphatidic acid binding / piecemeal microautophagy of the nucleus / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / phosphatidylserine binding / chloride channel activity / exocytosis / Neutrophil degranulation / chloride transmembrane transport / cell periphery / protein localization to plasma membrane / endocytosis / lipid binding / endoplasmic reticulum membrane / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Anoctamin / : / Calcium-activated chloride channel
Similarity search - Domain/homology
Chem-P5S / Increased sodium tolerance protein 2 / Oxysterol-binding protein homolog 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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
DepositionNov 12, 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
A: Oxysterol-binding protein homolog 6
C: Increased sodium tolerance protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3433
Polymers51,5512
Non-polymers7921
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.728, 175.697, 96.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

21A-882-

HOH

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Components

#1: Protein Oxysterol-binding protein homolog 6 / Lipid-transfer protein Osh6 / LTP / Oxysterol-binding phosphatidylserine transferase / Oxysterol- ...Lipid-transfer protein Osh6 / LTP / Oxysterol-binding phosphatidylserine transferase / Oxysterol-binding protein-related protein 6 / ORP 6 / OSBP-related protein 6


Mass: 48761.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OSH6, YKR003W, YK102 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02201
#2: Protein/peptide Increased sodium tolerance protein 2


Mass: 2789.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38250
#3: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO10P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 100mM BisTris pH 5.5, 200mM KCl, 75mM MgCl2, 28.5-29% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 41459 / % possible obs: 99.4 % / Redundancy: 7.18 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 18
Reflection shellResolution: 1.93→2 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 4022

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata processing
PHASERphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→32.43 Å / SU ML: 0.1942 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2132 1525 3.86 %
Rwork0.1851 37998 -
obs0.1862 39523 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.45 Å2
Refinement stepCycle: LAST / Resolution: 1.93→32.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 53 306 3781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663563
X-RAY DIFFRACTIONf_angle_d0.82214806
X-RAY DIFFRACTIONf_chiral_restr0.056506
X-RAY DIFFRACTIONf_plane_restr0.0085615
X-RAY DIFFRACTIONf_dihedral_angle_d19.68961398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.990.30151360.25843400X-RAY DIFFRACTION99.61
1.99-2.060.25181370.22473421X-RAY DIFFRACTION99.41
2.06-2.150.2531350.20783372X-RAY DIFFRACTION99.26
2.15-2.240.22841380.19853416X-RAY DIFFRACTION99
2.24-2.360.22441370.20023428X-RAY DIFFRACTION99.72
2.36-2.510.25111380.2073433X-RAY DIFFRACTION99.8
2.51-2.70.25261390.21543462X-RAY DIFFRACTION99.83
2.7-2.980.25271400.20873478X-RAY DIFFRACTION99.92
2.98-3.410.23491370.19383446X-RAY DIFFRACTION98.84
3.41-4.290.20511420.16333512X-RAY DIFFRACTION100

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