3IQL

Crystal structure of the rat endophilin-A1 SH3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 

wwPDB Validation   3D Report Full Report


This is version 1.1 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
Endophilin-A1A, B71Rattus norvegicusMutation(s): 0 
Gene Names: Sh3d2aSh3gl2Sh3p4
UniProt
Find proteins for O35179 (Rattus norvegicus)
Explore O35179 
Go to UniProtKB:  O35179
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.338α = 90
b = 34.156β = 107.79
c = 62.729γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance