5LW1

Crystal structure of DARPin-DARPin rigid fusion, variant DD_232_11_D12 in complex JNK1a1 and JIP1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Selective Inhibition of c-Jun N-Terminal Kinase 1 Determined by Rigid DARPin-DARPin Fusions.

Wu, Y.Honegger, A.Batyuk, A.Mittl, P.R.E.Pluckthun, A.

(2018) J.Mol.Biol. 430: 2128-2138

  • DOI: 10.1016/j.jmb.2017.10.032

  • PubMed Abstract: 
  • To untangle the complex signaling of the c-Jun N-terminal kinase (JNK) isoforms, we need tools that can selectively detect and inhibit individual isoforms. Because of the high similarity between JNK1, JNK2 and JNK3, it is very difficult to generate s ...

    To untangle the complex signaling of the c-Jun N-terminal kinase (JNK) isoforms, we need tools that can selectively detect and inhibit individual isoforms. Because of the high similarity between JNK1, JNK2 and JNK3, it is very difficult to generate small-molecule inhibitors with this discriminatory power. Thus, we have recently selected protein binders from the designed ankyrin repeat protein (DARPin) library which were indeed isoform-specific inhibitors of JNK1 with low nanomolar potency. Here we provide the structural basis for their isotype discrimination and their inhibitory action. All our previous attempts to generate crystal structures of complexes had failed. We have now made use of a technology we recently developed which consists of rigid fusion of an additional special DARPin, which acts as a crystallization enhancer. This can be rigidly fused with different geometries, thereby generating a range of alternative crystal packings. The structures reveal the molecular basis for isoform specificity of the DARPins and their ability to prevent JNK activation and may thus form the basis of further investigation of the JNK family as well as novel approaches to drug design.


    Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. Electronic address: plueckthun@bioc.uzh.ch.,Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DD_232_11_D12
A, D, G
326N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 8
B, E, H
373Homo sapiensMutation(s): 0 
Gene Names: MAPK8 (JNK1, PRKM8, SAPK1, SAPK1C)
EC: 2.7.11.24
Find proteins for P45983 (Homo sapiens)
Go to Gene View: MAPK8
Go to UniProtKB:  P45983
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
C-Jun-amino-terminal kinase-interacting protein 1
C, F, I
11Homo sapiensMutation(s): 0 
Gene Names: MAPK8IP1 (IB1, JIP1, PRKM8IP)
Find proteins for Q9UQF2 (Homo sapiens)
Go to Gene View: MAPK8IP1
Go to UniProtKB:  Q9UQF2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Pepstatin
L
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D, E, G, H, I
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADN
Query on ADN

Download SDF File 
Download CCD File 
B, E, H
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000557
Query on PRD_000557
LPepstatinOligopeptide / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 219.990α = 90.00
b = 141.760β = 97.83
c = 119.850γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030B_166676
European Research CouncilNEXTBINDERS

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-06-13
    Type: Data collection, Structure summary
  • Version 1.2: 2019-07-10
    Type: Data collection, Database references