9HDK | pdb_00009hdk

Structure of s.c.Osh6 in complex with Ist2 732-756 and POPS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural basis for lipid transport at membrane contact sites by the IST2-OSH6 complex.

Arndt, M.Schweri, A.Dutzler, R.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01660-z
  • Primary Citation of Related Structures:  
    9HDH, 9HDK, 9HHE, 9QJA, 9QJT, 9QJU

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry, University of Zurich, Zurich, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterol-binding protein homolog 6421Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OSH6YKR003WYK102
UniProt
Find proteins for Q02201 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02201 
Go to UniProtKB:  Q02201
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02201
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Increased sodium tolerance protein 2B [auth C]25Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38250 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38250 
Go to UniProtKB:  P38250
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38250
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5S (Subject of Investigation/LOI)
Query on P5S

Download Ideal Coordinates CCD File 
C [auth A]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.728α = 90
b = 175.697β = 90
c = 96.163γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
PHASERphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_215236

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release