5Z2M

Structure of Orp1L/Rab7 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.142 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A non-canonical GTPase interaction enables ORP1L-Rab7-RILP complex formation and late endosome positioning.

Ma, X.Liu, K.Li, J.Li, H.Li, J.Liu, Y.Yang, C.Liang, H.

(2018) J. Biol. Chem. 293: 14155-14164

  • DOI: 10.1074/jbc.RA118.001854
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endosomal transport represents the primary mode for intracellular trafficking and signaling transduction and thus has to be tightly controlled. The molecular processes controlling the endosomal positioning utilize several large protein complexes, one ...

    Endosomal transport represents the primary mode for intracellular trafficking and signaling transduction and thus has to be tightly controlled. The molecular processes controlling the endosomal positioning utilize several large protein complexes, one of which contains the small GTPase Rab7, Rab-interacting lysosomal protein (RILP), and oxysterol-binding protein-related protein 1 (ORP1L). Rab7 is known to interact with RILP through a canonical binding site termed the effector-interacting switch region, but it is not clear how Rab7 interacts with ORP1L, limiting our understanding of the overall process. Here, we report structural and biochemical investigation of the Rab7-ORP1L interaction. We found that, contrary to prior studies, the interaction between Rab7 and the N-terminal ankyrin repeat domain (ARD N ) of ORP1L is independent of Rab7's GTP- or GDP-binding state. Moreover, we show that Rab7 interacts with ORP1L ARD N via a unique region consisting of helix3 (α3) and 3 10 -helix 2 (η2). This architecture leaves the canonical effector-interacting switch regions available for RILP binding and thus allows formation of the ORP1L-Rab7-RILP tripartite complex. Mutational disruption of the interacting interface between ORP1L and Rab7 compromised the ability of ORP1L-Rab7-RILP to regulate the late endosome positioning. Collectively, our results again manifested the versatility in the interaction between GTPase and its effector.


    Organizational Affiliation

    State Key laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China, clyang@ynu.edu.cn.,Life Science Center and School of Life Sciences, Yunnan University, Kunming 650500, China, and.,State Key Laboratory of Utilization and Conservation of Bio-Resources in Yunnan and.,From the National Laboratory of Biomacromolecules, Institute of Biophysics and lianghh26@mail.sysu.edu.cn.,From the National Laboratory of Biomacromolecules, Institute of Biophysics and.,Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,State Key laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,Schools of Medicine and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxysterol-binding protein-related protein 1
B, D
138Mus musculusMutation(s): 0 
Gene Names: Osbpl1a (Orp1, Orp1a, Orp1l)
Find proteins for Q91XL9 (Mus musculus)
Go to UniProtKB:  Q91XL9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-7a
A, C
176Mus musculusMutation(s): 1 
Gene Names: Rab7a (Rab7)
Find proteins for P51150 (Mus musculus)
Go to UniProtKB:  P51150
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.142 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.222α = 90.00
b = 109.626β = 99.94
c = 77.811γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
iMOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references