3QBT

Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structural basis for Lowe syndrome caused by mutations in the Rab-binding domain of OCRL1.

Hou, X.Hagemann, N.Schoebel, S.Blankenfeldt, W.Goody, R.S.Erdmann, K.S.Itzen, A.

(2011) EMBO J 30: 1659-1670

  • DOI: 10.1038/emboj.2011.60
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The oculocerebrorenal syndrome of Lowe (OCRL), also called Lowe syndrome, is characterized by defects of the nervous system, the eye and the kidney. Lowe syndrome is a monogenetic X-linked disease caused by mutations of the inositol-5-phosphatase OCR ...

    The oculocerebrorenal syndrome of Lowe (OCRL), also called Lowe syndrome, is characterized by defects of the nervous system, the eye and the kidney. Lowe syndrome is a monogenetic X-linked disease caused by mutations of the inositol-5-phosphatase OCRL1. OCRL1 is a membrane-bound protein recruited to membranes via interaction with a variety of Rab proteins. The structural and kinetic basis of OCRL1 for the recognition of several Rab proteins is unknown. In this study, we report the crystal structure of the Rab-binding domain (RBD) of OCRL1 in complex with Rab8a and the kinetic binding analysis of OCRL1 with several Rab GTPases (Rab1b, Rab5a, Rab6a and Rab8a). In contrast to other effectors that bind their respective Rab predominantly via α-helical structure elements, the Rab-binding interface of OCRL1 consists mainly of the IgG-like β-strand structure of the ASPM-SPD-2-Hydin domain as well as one α-helix. Our results give a deeper structural understanding of disease-causing mutations of OCRL1 affecting Rab binding.


    Organizational Affiliation

    Department of Physical Biochemistry, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Inositol polyphosphate 5-phosphatase OCRL-1
B, D, F, H
140Homo sapiensMutation(s): 0 
Gene Names: INPP5FOCRLOCRL1
EC: 3.1.3.36 (PDB Primary Data), 3.1.3.56 (UniProt), 3.1.3.86 (UniProt)
Find proteins for Q01968 (Homo sapiens)
Go to UniProtKB:  Q01968
NIH Common Fund Data Resources
PHAROS  Q01968

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-8A
A, C, E, G
174Homo sapiensMutation(s): 0 
Gene Names: MELRAB8RAB8A
Find proteins for P61006 (Homo sapiens)
Go to UniProtKB:  P61006
NIH Common Fund Data Resources
PHAROS  P61006
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download CCD File 
A, C, E, G
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, C, E, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.147α = 90
b = 55.34β = 91.93
c = 173.836γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-29
    Changes: Database references