5TQW | pdb_00005tqw

CryoEM reconstruction of human IKK1, open conformation 1

  • 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., Biswas, 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: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 5TQW

This is version 1.6 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 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. 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.

Macromolecule Content 

  • Total Structure Weight: 150.29 kDa 
  • Atom Count: 9,192 
  • Modeled Residue Count: 1,128 
  • Deposited Residue Count: 1,310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inhibitor of nuclear factor kappa-B kinase subunit alpha
A, B
655Homo sapiensMutation(s): 3 
Gene Names: CHUKIKKATCF16
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
GTEx:  ENSG00000213341 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15111
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.11
MODEL REFINEMENTRosetta2015.12.57698
MODEL REFINEMENTPHENIXdev-2499

Structure Validation

View Full Validation Report



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
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references
  • Version 1.6: 2026-02-25
    Changes: Data collection, Structure summary