5LPN

Structure of human Rab10 in complex with the bMERB domain of Mical-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.

Rai, A.Oprisko, A.Campos, J.Fu, Y.Friese, T.Itzen, A.Goody, R.S.Gazdag, E.M.Muller, M.P.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.18675
  • Primary Citation of Related Structures:  
    5LPN, 5SZG, 5SZH, 5SZI, 5SZJ, 5SZK

  • PubMed Abstract: 

    In their active GTP-bound form, Rab proteins interact with proteins termed effector molecules. In this study, we have thoroughly characterized a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. Within our study, we show that these effectors display a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and that some of the effector domains can bind two Rab proteins via separate binding sites. Structural analysis allowed us to explain the specificity towards Rab8 family members and the presence of two similar Rab binding sites that must have evolved via gene duplication. This study is the first to thoroughly characterize a Rab effector protein that contains two separate Rab binding sites within a single domain, allowing Micals and EHBPs to bind two Rabs simultaneously, thus suggesting previously unknown functions of these effector molecules in endosomal trafficking.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-10
A, C
177Homo sapiensMutation(s): 0 
Gene Names: RAB10
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61026 (Homo sapiens)
Explore P61026 
Go to UniProtKB:  P61026
PHAROS:  P61026
GTEx:  ENSG00000084733 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61026
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-methionine sulfoxide oxidase MICAL1153Homo sapiensMutation(s): 0 
Gene Names: MICAL1MICALNICAL
EC: 1.14.13 (PDB Primary Data), 1.6.3.1 (UniProt), 1.14.13.225 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDZ2 (Homo sapiens)
Explore Q8TDZ2 
Go to UniProtKB:  Q8TDZ2
PHAROS:  Q8TDZ2
GTEx:  ENSG00000135596 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDZ2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.39α = 90
b = 59β = 90
c = 198.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB642, grant A4
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description