5TQY

CryoEM reconstruction of human IKK1, closed conformation 3

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): 

  • Deposited: 2016-10-24 Released: 2016-11-09 
  • Deposition Author(s): Lyumkis, D., Ghosh, G., Polley, S., Biswath, T., Huang, D., Passos, D.O.
  • Funding Organization(s): National Institutes of Health/Office of the Director; National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Cancer Institute; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesDP5 OD021396-01
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI064326
National Institutes of Health/National Cancer InstituteUnited StatesCA141722
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071862

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-11-30
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Data collection
  • Version 1.3: 2018-07-18
    Type: Data collection, Experimental preparation