PDBsum entry 3iql

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protein metals Protein-protein interface(s) links
Protein binding PDB id
Protein chains
66 a.a. *
_CL ×2
Waters ×192
* Residue conservation analysis
PDB id:
Name: Protein binding
Title: Crystal structure of the rat endophilin-a1 sh3 domain
Structure: Endophilin-a1. Chain: a, b. Synonym: endophilin-1, sh3 domain-containing grb2-like protein 2, sh3 domain protein 2a, sh3p4. Engineered: yes
Source: Rattus norvegicus. Brown rat,rat,rats. Organism_taxid: 10116. Gene: sh3d2a, sh3gl2, sh3p4. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.40Å     R-factor:   0.128     R-free:   0.154
Authors: J.F.Trempe,G.Kozlov,E.M.Camacho,K.Gehring
Key ref: J.F.Trempe et al. (2009). SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination. Mol Cell, 36, 1034-1047. PubMed id: 20064468
20-Aug-09     Release date:   10-Nov-09    
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Protein chains
Pfam   ArchSchema ?
O35179  (SH3G2_RAT) -  Endophilin-A1
352 a.a.
66 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     endocytosis   1 term 


Mol Cell 36:1034-1047 (2009)
PubMed id: 20064468  
SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination.
J.F.Trempe, C.X.Chen, K.Grenier, E.M.Camacho, G.Kozlov, P.S.McPherson, K.Gehring, E.A.Fon.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20940148 T.M.Durcan, M.Kontogiannea, T.Thorarinsdottir, L.Fallon, A.J.Williams, A.Djarmati, T.Fantaneanu, H.L.Paulson, and E.A.Fon (2011).
The Machado-Joseph disease-associated mutant form of ataxin-3 regulates parkin ubiquitination and stability.
  Hum Mol Genet, 20, 141-154.  
20440844 A.X.Song, C.J.Zhou, X.Guan, K.H.Sze, and H.Y.Hu (2010).
Solution structure of the N-terminal domain of DC-UbP/UBTD2 and its interaction with ubiquitin.
  Protein Sci, 19, 1104-1109.
PDB code: 2ksn
20410074 E.León, G.Navarro-Avilés, C.M.Santiveri, C.Flores-Flores, M.Rico, C.González, F.J.Murillo, M.Elías-Arnanz, M.A.Jiménez, and S.Padmanabhan (2010).
A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix.
  Nucleic Acids Res, 38, 5226-5241.
PDB code: 2kss
20541996 J.M.Winget, and T.Mayor (2010).
The diversity of ubiquitin recognition: hot spots and varied specificity.
  Mol Cell, 38, 627-635.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.