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- PDB-9hdh: Structure of s.c.Osh6 in complex with Ist2 732-761 and POPS -

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Basic information

Entry
Database: PDB / ID: 9hdh
TitleStructure of s.c.Osh6 in complex with Ist2 732-761 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: 1.84 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)52,8863
Polymers52,0942
Non-polymers7921
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-11 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.642, 176.251, 95.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

21A-692-

HOH

31A-752-

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: 3332.674 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.: 309 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 100mM BisTris pH 5.5, 200mM KCl, 20mM MgCl2, 28% - 30% 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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.84→32.42 Å / Num. obs: 44913 / % possible obs: 97.9 % / Redundancy: 6.73 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.91
Reflection shellResolution: 1.84→1.95 Å / Rmerge(I) obs: 1.541 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 12172 / % possible all: 87.1

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHASERphasing
PHENIX1.21.1 5286refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→32.42 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2097 -4.5 %
Rwork0.1795 --
obs-44425 97.9 %
Refinement stepCycle: LAST / Resolution: 1.84→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 53 309 3847
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.30120.32852046X-RAY DIFFRACTION67
1.89-1.940.25060.2483055X-RAY DIFFRACTION99

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