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 

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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: 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-10A, C177Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61026
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-methionine sulfoxide oxidase MICAL1B153Homo sapiensMutation(s): 0 
Gene Names: MICAL1, MICAL, NICAL
EC: 1.14.13 (PDB Primary Data), 1.14.13.225 (UniProt), 1.6.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDZ2 (Homo sapiens)
Explore Q8TDZ2 
Go to UniProtKB:  Q8TDZ2
PHAROS:  Q8TDZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDZ2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
F [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
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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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