5ZM7

Crystal structure of ORP1-ORD in complex with cholesterol at 3.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.278 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Allosteric enhancement of ORP1-mediated cholesterol transport by PI(4,5)P2/PI(3,4)P2.

Dong, J.Du, X.Wang, H.Wang, J.Lu, C.Chen, X.Zhu, Z.Luo, Z.Yu, L.Brown, A.J.Yang, H.Wu, J.W.

(2019) Nat Commun 10: 829-829

  • DOI: https://doi.org/10.1038/s41467-019-08791-0
  • Primary Citation of Related Structures:  
    5ZM5, 5ZM6, 5ZM7

  • PubMed Abstract: 

    Phosphatidylinositol phosphates (PIPs) and cholesterol are known to regulate the function of late endosomes and lysosomes (LELs), and ORP1L specifically localizes to LELs. Here, we show in vitro that ORP1 is a PI(4,5)P 2 - or PI(3,4)P 2 -dependent cholesterol transporter, but cannot transport any PIPs. In cells, both ORP1L and PI(3,4)P 2 are required for the efficient removal of cholesterol from LELs. Structures of the lipid-binding domain of ORP1 (ORP1-ORD) in complex with cholesterol or PI(4,5)P 2 display open conformations essential for ORP function. PI(4,5)P 2 /PI(3,4)P 2 can facilitate ORP1-mediated cholesterol transport by promoting membrane targeting and cholesterol extraction. Thus, our work unveils a distinct mechanism by which PIPs may allosterically enhance OSBP/ORPs-mediated transport of major lipid species such as cholesterol.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterol-binding protein-related protein 1436Homo sapiensMutation(s): 0 
Gene Names: OSBPL1AORP1OSBP8OSBPL1OSBPL1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXW6 (Homo sapiens)
Explore Q9BXW6 
Go to UniProtKB:  Q9BXW6
PHAROS:  Q9BXW6
GTEx:  ENSG00000141447 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXW6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
B [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.278 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.253α = 90
b = 149.253β = 90
c = 149.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0502004

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description