4G3D

Crystal structure of human NF-kappaB inducing kinase (NIK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.201 

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, D, E
371Homo sapiensMutation(s): 0 
Gene Names: MAP3K14 (NIK)
EC: 2.7.11.25
Find proteins for Q99558 (Homo sapiens)
Go to Gene View: MAP3K14
Go to UniProtKB:  Q99558
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.746α = 90.00
b = 145.851β = 90.00
c = 230.818γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Web-Icedata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

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View more in-depth experimental data

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