hMiro EF hand and cGTPase domains in the GMPPCP-bound state

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Model: experimental
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Structural insights into Parkin substrate lysine targeting from minimal Miro substrates.

Klosowiak, J.L.Park, S.Smith, K.P.French, M.E.Focia, P.J.Freymann, D.M.Rice, S.E.

(2016) Sci Rep 6: 33019-33019

  • DOI: https://doi.org/10.1038/srep33019
  • Primary Citation of Related Structures:  
    5KSO, 5KSP, 5KSY, 5KSZ, 5KTY, 5KU1, 5KUT

  • PubMed Abstract: 

    Hereditary Parkinson's disease is commonly caused by mutations in the protein kinase PINK1 or the E3 ubiquitin ligase Parkin, which function together to eliminate damaged mitochondria. PINK1 phosphorylates both Parkin and ubiquitin to stimulate ubiquitination of dozens of proteins on the surface of the outer mitochondrial membrane. However, the mechanisms by which Parkin recognizes specific proteins for modification remain largely unexplored. Here, we show that the C-terminal GTPase (cGTPase) of the Parkin primary substrate human Miro is necessary and sufficient for efficient ubiquitination. We present several new X-ray crystal structures of both human Miro1 and Miro2 that reveal substrate recognition and ubiquitin transfer to be specific to particular protein domains and lysine residues. We also provide evidence that Parkin substrate recognition is functionally separate from substrate modification. Finally, we show that prioritization for modification of a specific lysine sidechain of the cGTPase (K572) within human Miro1 is dependent on both its location and chemical microenvironment. Activation of Parkin by phosphorylation or by binding of pUb is required for prioritization of K572 for modification, suggesting that Parkin activation and acquisition of substrate specificity are coupled.

  • Organizational Affiliation

    Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial Rho GTPase 1424Homo sapiensMutation(s): 0 
Gene Names: RHOT1ARHT1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXI2 (Homo sapiens)
Explore Q8IXI2 
Go to UniProtKB:  Q8IXI2
GTEx:  ENSG00000126858 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IXI2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.18α = 90
b = 74.18β = 90
c = 218.859γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description