6BYM

Crystal structure of the sterol-bound second StART domain of yeast Lam4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

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This is version 1.7 of the entry. See complete history


Literature

Structural basis of sterol binding and transport by a yeast StARkin domain.

Jentsch, J.A.Kiburu, I.Pandey, K.Timme, M.Ramlall, T.Levkau, B.Wu, J.Eliezer, D.Boudker, O.Menon, A.K.

(2018) J Biol Chem 293: 5522-5531

  • DOI: https://doi.org/10.1074/jbc.RA118.001881
  • Primary Citation of Related Structures:  
    6BYD, 6BYM

  • PubMed Abstract: 

    The StARkin superfamily comprises proteins with steroidogenic acute regulatory protein-related lipid transfer (StART) domains that are implicated in intracellular, non-vesicular lipid transport. A new family of membrane-anchored StARkins was recently identified, including six members, Lam1-Lam6, in the yeast Saccharomyces cerevisiae. Lam1-Lam4 are anchored to the endoplasmic reticulum (ER) membrane at sites where the ER is tethered to the plasma membrane and proposed to be involved in sterol homeostasis in yeast. To better understand the biological roles of these proteins, we carried out a structure-function analysis of the second StARkin domain of Lam4, here termed Lam4S2. NMR experiments indicated that Lam4S2 undergoes specific conformational changes upon binding sterol, and fluorescence-based assays revealed that it catalyzes sterol transport between vesicle populations in vitro , exhibiting a preference for vesicles containing anionic lipids. Using such vesicles, we found that sterols are transported at a rate of ∼50 molecules per Lam4S2 per minute. Crystal structures of Lam4S2, with and without bound sterol, revealed a largely hydrophobic but surprisingly accessible sterol-binding pocket with the 3-OH group of the sterol oriented toward its base. Single or multiple alanine or aspartic acid replacements of conserved lysine residues in a basic patch on the surface of Lam4S2 near the likely sterol entry/egress site strongly attenuated sterol transport. Our results suggest that Lam4S2 engages anionic membranes via a basic surface patch, enabling "head-first" entry of sterol into the binding pocket followed by partial closure of the entryway. Reversal of these steps enables sterol egress.


  • Organizational Affiliation

    From the Departments of Biochemistry and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sterol-binding protein
A, B
203Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LAM4SCKG_4597
Membrane Entity: Yes 
UniProt
Find proteins for P38800 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38800 
Go to UniProtKB:  P38800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38800
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.179α = 111.21
b = 47.301β = 101.63
c = 55.996γ = 100.33
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGraduiertenkolleg 2098, Project 11
Qatar National Research FundQatarNPRP 7-082-1-014

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2018-01-31
    Changes: Structure summary
  • Version 1.3: 2018-02-14
    Changes: Author supporting evidence
  • Version 1.4: 2018-03-07
    Changes: Database references
  • Version 1.5: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.6: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.7: 2024-03-13
    Changes: Data collection, Database references, Refinement description