6L1D | pdb_00006l1d

Structure of human StAR-related lipid transfer protein 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural analysis of human sterol transfer protein STARD4.

Tan, L.Tong, J.Chun, C.Im, Y.J.

(2019) Biochem Biophys Res Commun 520: 466-472

  • DOI: https://doi.org/10.1016/j.bbrc.2019.10.054
  • Primary Citation Related Structures: 
    6L1D, 6L1M

  • PubMed Abstract: 

    The steroidogenic acute regulatory protein (StAR)-related lipid transfer domain-4 (STARD4) is a sterol-binding protein that is involved in cholesterol homeostasis by intracellular sterol transport. In this work, we determined the crystal structures of human STARD4 and its Ω1-loop mutant in apo forms at 1.95 and 1.7 Å resolutions, respectively. The structure of human STARD4 displays a conserved α-helix/β-grip fold containing a deep hydrophobic pocket. The Ω1-loop which serves as a lid for the hydrophobic pocket has a closed conformation. The shape of the sterol-binding cavity in the closed form is not complementary to accommodate cholesterol, suggesting that a conformational change of the Ω1-loop is essential for sterol binding. The human STARD4 displayed sterol transfer activity between liposomes, and the mutations in the Ω1-loop and the hydrophobic wall abolished the transfer activity. This study confirms the structural conservation of the STARD4 subfamily proteins and the flexibility of the Ω1-loop and helix α4 required for sterol transport.


  • Organizational Affiliation
    • College of Pharmacy, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea.

Macromolecule Content 

  • Total Structure Weight: 47.77 kDa 
  • Atom Count: 3,720 
  • Modeled Residue Count: 400 
  • Deposited Residue Count: 420 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
StAR-related lipid transfer protein 4
A, B
210Homo sapiensMutation(s): 1 
Gene Names: STARD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DR4 (Homo sapiens)
Explore Q96DR4 
Go to UniProtKB:  Q96DR4
PHAROS:  Q96DR4
GTEx:  ENSG00000164211 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96DR4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.77α = 90
b = 93.77β = 90
c = 73.275γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description