6BYD | pdb_00006byd

Crystal structure of the second StART domain of yeast Lam4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.248 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6BYD

This is version 1.5 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 Biological Chem 293: 5522-5531

  • DOI: https://doi.org/10.1074/jbc.RA118.001881
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 23.04 kDa 
  • Atom Count: 1,601 
  • Modeled Residue Count: 197 
  • Deposited Residue Count: 203 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane-anchored lipid-binding protein LAM4203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LAM4LTC3YHR080C
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

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.601α = 90
b = 67.923β = 90
c = 132.042γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL2Mapphasing

Structure Validation

View Full Validation Report



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: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-07
    Changes: Database references
  • Version 1.3: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2024-10-23
    Changes: Data collection, Database references, Structure summary