Crystal structure of the second StARkin domain of Lam2 in complex with ergosterol

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites

Tong, J.Manik, M.K.Im, Y.J.

(2018) Proc Natl Acad Sci U S A 115: E856-E865

  • DOI: https://doi.org/10.1073/pnas.1719709115
  • Primary Citation of Related Structures:  
    5YQI, 5YQJ, 5YQP, 5YQQ, 5YQR, 5YS0

  • PubMed Abstract: 

    Membrane contact sites (MCSs) in eukaryotic cells are hotspots for lipid exchange, which is essential for many biological functions, including regulation of membrane properties and protein trafficking. Lipid transfer proteins anchored at membrane contact sites (LAMs) contain sterol-specific lipid transfer domains [StARkin domain (SD)] and multiple targeting modules to specific membrane organelles. Elucidating the structural mechanisms of targeting and ligand recognition by LAMs is important for understanding the interorganelle communication and exchange at MCSs. Here, we determined the crystal structures of the yeast Lam6 pleckstrin homology (PH)-like domain and the SDs of Lam2 and Lam4 in the apo form and in complex with ergosterol. The Lam6 PH-like domain displays a unique PH domain fold with a conserved N-terminal α-helix. The Lam6 PH-like domain lacks the basic surface for phosphoinositide binding, but contains hydrophobic patches on its surface, which are critical for targeting to endoplasmic reticulum (ER)-mitochondrial contacts. Structures of the LAM SDs display a helix-grip fold with a hydrophobic cavity and a flexible Ω1-loop as a lid. Ergosterol is bound to the pocket in a head-down orientation, with its hydrophobic acyl group located in the tunnel entrance. The Ω1-loop in an open conformation is essential for ergosterol binding by direct hydrophobic interaction. Structural comparison suggested that the sterol binding mode of the Lam2 SD2 is likely conserved among the sterol transfer proteins of the StARkin superfamily. Structural models of full-length Lam2 correlated with the sterol transport function at the membrane contact sites.

  • Organizational Affiliation

    College of Pharmacy, Chonnam National University, Bukgu, Gwangju, 61186, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane-anchored lipid-binding protein YSP2
A, B, C
170Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YSP2LAM2LTC4YDR326C
Membrane Entity: Yes 
Find proteins for Q06681 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06681 
Go to UniProtKB:  Q06681
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06681
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.717α = 90
b = 70.315β = 103.14
c = 42.508γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1A2B4004914

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description