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 

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
  • Primary Citation of Related Structures:  

  • 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: 
    • 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
    • IB1, a JIP-1-related nuclear protein present in insulin-secreting cells
      Bonny, C.,Nicod, P.,Waeber, G.
      (1998) J.Biol.Chem. 273: 1843
    • 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
    • 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: Mapk8ip1 (Ib1, Jip1, Mapk8ip)
Find proteins for Q9R237 (Rattus norvegicus)
Go to UniProtKB:  Q9R237
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B, C, E, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
P6G
Query on P6G
Download SDF File 
Download CCD File 
A, D, G
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
SO2
Query on SO2
Download SDF File 
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 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.594α = 90.00
b = 81.591β = 90.00
c = 89.733γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
TRUNCATEdata reduction
TRUNCATEdata scaling
CNSphasing
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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