2KNB

Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination.

Trempe, J.F.Chen, C.X.Grenier, K.Camacho, E.M.Kozlov, G.McPherson, P.S.Gehring, K.Fon, E.A.

(2009) Mol Cell 36: 1034-1047

  • DOI: 10.1016/j.molcel.2009.11.021
  • Primary Citation of Related Structures:  
    2KNB, 3IQL

  • PubMed Abstract: 
  • Mutations in the parkin gene are responsible for a common inherited form of Parkinson's disease (PD). Parkin is a RING-type E3 ubiquitin ligase with an N-terminal ubiquitin-like domain (Ubl). We report here that the parkin Ubl binds SH3 domains from endocytic BAR proteins such as endophilin-A with an affinity comparable to proline-rich domains (PRDs) from well-established SH3 partners ...

    Mutations in the parkin gene are responsible for a common inherited form of Parkinson's disease (PD). Parkin is a RING-type E3 ubiquitin ligase with an N-terminal ubiquitin-like domain (Ubl). We report here that the parkin Ubl binds SH3 domains from endocytic BAR proteins such as endophilin-A with an affinity comparable to proline-rich domains (PRDs) from well-established SH3 partners. The NMR structure of the Ubl-SH3 complex identifies the PaRK extension, a unique C-terminal motif in the parkin Ubl required for SH3 binding and for parkin-mediated ubiquitination of endophilin-A in vitro. In nerve terminals, conditions that promote phosphorylation enhance the interaction between parkin and endophilin-A and increase the levels of ubiquitinated proteins within PRD-associated synaptic protein complexes in wild-type but not parkin knockout brain. The findings identify a pathway for the recruitment of synaptic substrates to parkin with the potential to explain the defects in synaptic transmission observed in recessive forms of PD.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, Québec, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkinA81Rattus norvegicusMutation(s): 0 
Gene Names: Park2Prkn
EC: 6.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
UniProt
Find proteins for Q9JK66 (Rattus norvegicus)
Explore Q9JK66 
Go to UniProtKB:  Q9JK66
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Endophilin-A1B71Rattus norvegicusMutation(s): 0 
Gene Names: Sh3gl2Sh3d2aSh3p4
UniProt
Find proteins for O35179 (Rattus norvegicus)
Explore O35179 
Go to UniProtKB:  O35179
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2KNB Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references