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 
  • R-Value Observed: 0.187 

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:  
    4H36, 4H39, 4H3B

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10A, C356Homo sapiensMutation(s): 0 
Gene Names: MAPK10JNK3JNK3APRKM10SAPK1B
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SH3 domain-binding protein 5B, D10Homo sapiensMutation(s): 0 
Gene Names: SH3BP5SAB
UniProt & NIH Common Fund Data Resources
Find proteins for O60239 (Homo sapiens)
Explore O60239 
Go to UniProtKB:  O60239
PHAROS:  O60239
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.52α = 90
b = 84.52β = 90
c = 127.25γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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