5EBZ

Crystal structure of human IKK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Activation of IKK1/ alpha.

Polley, S.Passos, D.O.Huang, D.B.Mulero, M.C.Mazumder, A.Biswas, T.Verma, I.M.Lyumkis, D.Ghosh, G.

(2016) Cell Rep 17: 1907-1914

  • DOI: 10.1016/j.celrep.2016.10.067
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Distinct signaling pathways activate the NF-κB family of transcription factors. The canonical NF-κB-signaling pathway is mediated by IκB kinase 2/β (IKK2/β), while the non-canonical pathway depends on IKK1/α. The structural and biochemical bases for ...

    Distinct signaling pathways activate the NF-κB family of transcription factors. The canonical NF-κB-signaling pathway is mediated by IκB kinase 2/β (IKK2/β), while the non-canonical pathway depends on IKK1/α. The structural and biochemical bases for distinct signaling by these otherwise highly similar IKKs are unclear. We report single-particle cryoelectron microscopy (cryo-EM) and X-ray crystal structures of human IKK1 in dimeric (∼150 kDa) and hexameric (∼450 kDa) forms. The hexamer, which is the representative form in the crystal but comprises only ∼2% of the particles in solution by cryo-EM, is a trimer of IKK1 dimers. While IKK1 hexamers are not detectable in cells, the surface that supports hexamer formation is critical for IKK1-dependent cellular processing of p100 to p52, the hallmark of non-canonical NF-κB signaling. Comparison of this surface to that in IKK2 indicates significant divergence, and it suggests a fundamental role for this surface in signaling by these kinases through distinct pathways.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.,Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address: dlyumkis@salk.edu.,Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093, USA. Electronic address: gghosh@ucsd.edu.,Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093, USA; Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inhibitor of nuclear factor kappa-B kinase subunit alpha
A, B, C, D, E, F, G, H, I, J, K, L
655Homo sapiensMutation(s): 2 
Gene Names: CHUK (IKKA, TCF16)
EC: 2.7.11.10
Find proteins for O15111 (Homo sapiens)
Go to Gene View: CHUK
Go to UniProtKB:  O15111
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5LS
Query on 5LS

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
[(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-4,6-bis(oxidanyl)-5-sulfooxy-oxan-3-yl] hydrogen sulfate
C6 H12 O12 S2
JGSBCXNEVHAJNT-RXRWUWDJSA-N
 Ligand Interaction
5TK
Query on 5TK

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Download CCD File 
A, C, G, I
(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-oxidanylsulfanyloxy-oxane-2,3,4-triol
C6 H12 O7 S
LYKOPFRBCNKSPJ-UKFBFLRUSA-N
 Ligand Interaction
GLC
Query on GLC

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
5TM
Query on 5TM

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Download CCD File 
B, C, G, J
[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-2,5-bis(oxidanyl)-4-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate
C6 H12 O10 S2
AAAMJICHKUQUOZ-DVKNGEFBSA-N
 Ligand Interaction
Z4K
Query on Z4K

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Download CCD File 
B, C, H, J
2-O-sulfo-alpha-D-glucopyranose
C6 H12 O9 S
MOGKHCGKIJXABF-DVKNGEFBSA-N
 Ligand Interaction
PDX
Query on PDX

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
2,3-DI-O-SULFO-ALPHA-D-GLUCOPYRANOSE
C6 H12 O12 S2
ORUZACWROKWTRH-DVKNGEFBSA-N
 Ligand Interaction
5TH
Query on 5TH

Download SDF File 
Download CCD File 
A, C, G, I
[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4-bis(oxidanyl)-5-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate
C6 H12 O10 S2
OPPADQYGDDCNPC-RXRWUWDJSA-N
 Ligand Interaction
5TJ
Query on 5TJ

Download SDF File 
Download CCD File 
A, D, H, I
[(2~{R},3~{R},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-5,6-bis(oxidanyl)-3-oxidanylsulfanyloxy-oxan-4-yl] hydrogen sulfate
C6 H12 O10 S2
MQAJXHKPMARBQJ-UKFBFLRUSA-N
 Ligand Interaction
5TL
Query on 5TL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
2-azanyl-5-phenyl-3-(4-sulfamoylphenyl)benzamide
C19 H17 N3 O3 S
IVJPEEHVYKDQEO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5TLIC50: 1000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 174.510α = 90.00
b = 186.940β = 98.84
c = 275.830γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA141722

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence