6DJW

Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of parkin activation by phosphorylation.

Sauve, V.Sung, G.Soya, N.Kozlov, G.Blaimschein, N.Miotto, L.S.Trempe, J.F.Lukacs, G.L.Gehring, K.

(2018) Nat Struct Mol Biol 25: 623-630

  • DOI: 10.1038/s41594-018-0088-7
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mutations in the ubiquitin ligase parkin are responsible for a familial form of Parkinson's disease. Parkin and the PINK1 kinase regulate a quality-control system for mitochondria. PINK1 phosphorylates ubiquitin on the outer membrane of damaged mitoc ...

    Mutations in the ubiquitin ligase parkin are responsible for a familial form of Parkinson's disease. Parkin and the PINK1 kinase regulate a quality-control system for mitochondria. PINK1 phosphorylates ubiquitin on the outer membrane of damaged mitochondria, thus leading to recruitment and activation of parkin via phosphorylation of its ubiquitin-like (Ubl) domain. Here, we describe the mechanism of parkin activation by phosphorylation. The crystal structure of phosphorylated Bactrocera dorsalis (oriental fruit fly) parkin in complex with phosphorylated ubiquitin and an E2 ubiquitin-conjugating enzyme reveals that the key activating step is movement of the Ubl domain and release of the catalytic RING2 domain. Hydrogen/deuterium exchange and NMR experiments with the various intermediates in the activation pathway confirm and extend the interpretation of the crystal structure to mammalian parkin. Our results rationalize previously unexplained Parkinson's disease mutations and the presence of internal linkers that allow large domain movements in parkin.


    Organizational Affiliation

    McGill Centre for Structural Biology, McGill University, Montreal, Quebec, Canada. kalle.gehring@mcgill.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RBR-type E3 ubiquitin transferase,RBR-type E3 ubiquitin transferase
A
349Bactrocera dorsalisMutation(s): 0 
Gene Names: PRKN2
EC: 2.3.2.31
Find proteins for A0A034W4L8 (Bactrocera dorsalis)
Go to UniProtKB:  A0A034W4L8
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
74Bos taurusMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
Find proteins for P62992 (Bos taurus)
Go to UniProtKB:  P62992
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 L3
C
159Homo sapiensMutation(s): 1 
Gene Names: UBE2L3UBCE7UBCH7
EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens)
Go to UniProtKB:  P68036
NIH Common Fund Data Resources
PHAROS  P68036
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.606α = 90
b = 134.606β = 90
c = 86.193γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-125924
Michael J. Fox FoundationUnited States12144

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence