4H3B

Crystal Structure of JNK3 in Complex with SAB Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Mechanisms of Allostery and Autoinhibition in JNK Family Kinases.

Laughlin, J.D.Nwachukwu, J.C.Figuera-Losada, M.Cherry, L.Nettles, K.W.Lograsso, P.V.

(2012) Structure 20: 2174-2184

  • DOI: 10.1016/j.str.2012.09.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • c-Jun N-terminal (JNK) family kinases have a common peptide-docking site used by upstream activating kinases, substrates, scaffold proteins, and phosphatases, where the ensemble of bound proteins determines signaling output. Although there are many J ...

    c-Jun N-terminal (JNK) family kinases have a common peptide-docking site used by upstream activating kinases, substrates, scaffold proteins, and phosphatases, where the ensemble of bound proteins determines signaling output. Although there are many JNK structures, little is known about mechanisms of allosteric regulation between the catalytic and peptide-binding sites, and the activation loop, whose phosphorylation is required for catalytic activity. Here, we compare three structures of unliganded JNK3 bound to different peptides. These were compared as a class to structures that differ in binding of peptide, small molecule ligand, or conformation of the kinase activation loop. Peptide binding induced an inhibitory interlobe conformer that was reversed by alterations in the activation loop. Structure class analysis revealed the subtle structural mechanisms for allosteric signaling between the peptide-binding site and activation loop. Biochemical data from isothermal calorimetry, fluorescence energy transfer, and enzyme inhibition demonstrated affinity differences among the three peptides that were consistent with structural observations.


    Organizational Affiliation

    Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 10
A, C
356Homo sapiensMutation(s): 0 
Gene Names: MAPK10 (JNK3, JNK3A, PRKM10, SAPK1B)
EC: 2.7.11.24
Find proteins for P53779 (Homo sapiens)
Go to Gene View: MAPK10
Go to UniProtKB:  P53779
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SH3 domain-binding protein 5
B, D
10Homo sapiensMutation(s): 0 
Gene Names: SH3BP5 (SAB)
Find proteins for O60239 (Homo sapiens)
Go to Gene View: SH3BP5
Go to UniProtKB:  O60239
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 84.520α = 90.00
b = 84.520β = 90.00
c = 127.250γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
Blu-Icedata collection
PHENIXphasing
PHENIXmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2012-11-28
    Type: Database references
  • Version 1.2: 2012-12-26
    Type: Database references
  • Version 1.3: 2015-06-17
    Type: Structure summary