5TQY

CryoEM reconstruction of human IKK1, closed conformation 3

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

  • 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 (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1016/j.celrep.2016.10.067
  • Primary Citation of Related Structures:  
    5EBZ, 5TQW, 5TQX, 5TQY

  • 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 by these otherwise highly similar IKKs are unclear ...

    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. Electronic address: gghosh@ucsd.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inhibitor of nuclear factor kappa-B kinase subunit alpha
A, B
655Homo sapiensMutation(s): 3 
Gene Names: CHUK, IKKA, TCF16
EC: 2.7.11.10
UniProt & NIH Common Fund Data Resources
Find proteins for O15111 (Homo sapiens)
Explore O15111 
Go to UniProtKB:  O15111
PHAROS:  O15111
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15111
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta2015.12.57698
MODEL REFINEMENTPHENIXdev-2499
RECONSTRUCTIONFREALIGN9.11

Structure Validation

View Full Validation Report



View more in-depth experimental data
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 Diseases (NIH/NIAID)United StatesAI064326
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA141722
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071862

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-11-30
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence