4G3E

Crystal structure of murine NF-kappaB inducing kinase (NIK) bound to a 6-alkynylindoline (cmp1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the catalytic domain of the NF-kappaB inducing kinase reveals a narrow but flexible active site.

de Leon-Boenig, G.Bowman, K.K.Feng, J.A.Crawford, T.Everett, C.Franke, Y.Oh, A.Stanley, M.Staben, S.T.Starovasnik, M.A.Wallweber, H.J.Wu, J.Wu, L.C.Johnson, A.R.Hymowitz, S.G.

(2012) Structure 20: 1704-1714

  • DOI: 10.1016/j.str.2012.07.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The NF-κB inducing kinase (NIK) regulates the non-canonical NF-κB pathway downstream of important clinical targets including BAFF, RANKL, and LTβ. Despite numerous genetic studies associating dysregulation of this pathway with autoimmune diseases and ...

    The NF-κB inducing kinase (NIK) regulates the non-canonical NF-κB pathway downstream of important clinical targets including BAFF, RANKL, and LTβ. Despite numerous genetic studies associating dysregulation of this pathway with autoimmune diseases and hematological cancers, detailed molecular characterization of this central signaling node has been lacking. We undertook a systematic cloning and expression effort to generate soluble, well-behaved proteins encompassing the kinase domains of human and murine NIK. Structures of the apo NIK kinase domain from both species reveal an active-like conformation in the absence of phosphorylation. ATP consumption and peptide phosphorylation assays confirm that phosphorylation of NIK does not increase enzymatic activity. Structures of murine NIK bound to inhibitors possessing two different chemotypes reveal conformational flexibility in the gatekeeper residue controlling access to a hydrophobic pocket. Finally, a single amino acid difference affects the ability of some inhibitors to bind murine and human NIK with the same affinity.


    Organizational Affiliation

    Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NF-kappa-beta-inducing kinase
A, B
352Mus musculusMutation(s): 0 
Gene Names: Map3k14 (Nik)
EC: 2.7.11.25
Find proteins for Q9WUL6 (Mus musculus)
Go to UniProtKB:  Q9WUL6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
0WC
Query on 0WC

Download SDF File 
Download CCD File 
A, B
(2R)-4-[1-(2-amino-5-chloropyrimidin-4-yl)-2,3-dihydro-1H-indol-6-yl]-2-(1,3-thiazol-2-yl)but-3-yn-2-ol
C19 H16 Cl N5 O S
OKFYOOFXVBCIIP-LJQANCHMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0WCKi: 4.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.189 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 143.145α = 90.00
b = 143.145β = 90.00
c = 45.151γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
Web-Icedata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Refinement description, Structure summary