2FPE

Conserved dimerization of the ib1 src-homology 3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A unique set of SH3-SH3 interactions controls IB1 homodimerization

Kristensen, O.Guenat, S.Dar, I.Allaman-Pillet, N.Abderrahmani, A.Ferdaoussi, M.Roduit, R.Maurer, F.Beckmann, J.S.Kastrup, J.S.Gajhede, M.Bonny, C.

(2006) EMBO J 25: 785-797

  • DOI: 10.1038/sj.emboj.7600982
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Islet-brain 1 (IB1 or JIP-1) is a scaffold protein that interacts with components of the c-Jun N-terminal kinase (JNK) signal-transduction pathway. IB1 is expressed at high levels in neurons and in pancreatic beta-cells, where it controls expression ...

    Islet-brain 1 (IB1 or JIP-1) is a scaffold protein that interacts with components of the c-Jun N-terminal kinase (JNK) signal-transduction pathway. IB1 is expressed at high levels in neurons and in pancreatic beta-cells, where it controls expression of several insulin-secretory components and secretion. IB1 has been shown to homodimerize, but neither the molecular mechanisms nor the function of dimerization have yet been characterized. Here, we show that IB1 homodimerizes through a novel and unique set of Src homology 3 (SH3)-SH3 interactions. X-ray crystallography studies show that the dimer interface covers a region usually engaged in PxxP-mediated ligand recognition, even though the IB1 SH3 domain lacks this motif. The highly stable IB1 homodimer can be significantly destabilized in vitro by three individual point mutations directed against key residues involved in dimerization. Each mutation reduces IB1-dependent basal JNK activity in 293T cells. Impaired dimerization also results in a reduction in glucose transporter type 2 expression and in glucose-dependent insulin secretion in pancreatic beta-cells. Taken together, these results indicate that IB1 homodimerization through its SH3 domain has pleiotropic effects including regulation of the insulin secretion process.


    Related Citations: 
    • A cytoplasmic inhibitor of the JNK signal transduction pathway
      Dickens, M., Rogers, J.S., Cavanagh, J., Raitano, A., Xia, Z., Halpern, J.R., Greenberg, M.E., Sawyers, C.L., Davis, R.J.
      (1997) Science 277: 693
    • IB1, a JIP-1-related nuclear protein present in insulin-secreting cells
      Bonny, C., Nicod, P., Waeber, G.
      (1998) J Biol Chem 273: 1843
    • Recruitment of JNK to JIP1 and JNK-dependent JIP1 phosphorylation regulates JNK module dynamics and activation
      Nihalani, D., Wong, H.N., Holzman, L.B.
      (2003) J Biol Chem 278: 28694
    • The JIP group of mitogen-activated protein kinase scaffold proteins
      Yasuda, J., Whitmarsh, A.J., Cavanagh, J., Sharma, M., Davis, R.J.
      (1999) Mol Cell Biol 19: 7245

    Organizational Affiliation

    Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Copenhagen, Denmark. ok@dfuni.dk



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-jun-amino-terminal kinase interacting protein 1
A, B, C, D, E, F, G, H
62Rattus norvegicusMutation(s): 0 
Gene Names: Mapk8ip1Ib1Jip1Mapk8ip
Find proteins for Q9R237 (Rattus norvegicus)
Go to UniProtKB:  Q9R237
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download CCD File 
A, D, G
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, E, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SO2
Query on SO2

Download CCD File 
F
SULFUR DIOXIDE
O2 S
RAHZWNYVWXNFOC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,D,E,F,G,H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.594α = 90
b = 81.591β = 90
c = 89.733γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
CNSrefinement
CCP4data scaling
TRUNCATEdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description