6IYB

Structure of human ORP1 ANK - Rab7 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting.

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

(2019) PLoS One 14: e0211724-e0211724

  • DOI: https://doi.org/10.1371/journal.pone.0211724
  • Primary Citation of Related Structures:  
    6IYB

  • PubMed Abstract: 

    Oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) constitute a family of lipid transfer proteins conserved in eukaryotes. ORP1 transports cholesterol at the interface between the late endosomes/lysosomes (LELs) and the endoplasmic reticulum (ER). ORP1 is targeted to the endosomal membranes by forming a tripartite complex with the LE GTPase Rab7 and its effector RILP (Rab7-interacting lysosomal protein). Here, we determined the crystal structure of human ORP1 ANK domain in complex with the GTP-bound form of Rab7. ORP1 ANK binds to the helix α3 of Rab7 located away from the switching regions, which makes the interaction independent of the nucleotide-binding state of Rab7. Thus, the effector-interacting switch regions of Rab7 are accessible for RILP binding, allowing formation of the ORP1-Rab7-RILP complex. ORP1 ANK binds to Rab7 and the Rab7-RILP complex with similar micro-molar affinities, which is consistent with the independence binding of ORP1 and RILP to Rab7. The structural model of the ORP1-Rab7-RILP complex correlates with the recruitment of ORP1 at the LEL-ER interface and the role in lipid transport and regulation.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-7a
A, C
199Homo sapiensMutation(s): 1 
Gene Names: RAB7A
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51149 (Homo sapiens)
Explore P51149 
Go to UniProtKB:  P51149
PHAROS:  P51149
GTEx:  ENSG00000075785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51149
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterol-binding protein-related protein 1
B, D
154Homo sapiensMutation(s): 0 
Gene Names: OSBPL1A
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.136α = 90
b = 117.222β = 90
c = 130.476γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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: 2019-03-13
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description