1U6D | pdb_00001u6d

Crystal structure of the Kelch domain of human Keap1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.182 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.148 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1U6D

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the kelch domain of human keap1

Li, X.Zhang, D.Hannink, M.Beamer, L.J.

(2004) J Biological Chem 279: 54750-54758

  • DOI: https://doi.org/10.1074/jbc.M410073200
  • Primary Citation Related Structures: 
    1U6D

  • PubMed Abstract: 

    Keap1 is a substrate adaptor protein for an ubiquitin ligase complex that targets the Nrf2 transcription factor for degradation. Keap1 binds Nrf2 through its C-terminal Kelch domain, which contains six copies of the evolutionarily conserved kelch repeat sequence motif. The structure of the Kelch domain from human Keap1 has been determined by x-ray crystallography to a resolution of 1.85 A. The Kelch domain forms a 6-bladed beta-propeller structure, with residues at the C terminus forming the first strand in the first blade. Key structural roles have been identified for the highly conserved glycine, tyrosine, and tryptophan residues that define the kelch repeat sequence motif. In addition, we show that substitution of a single amino acid located within a loop that extends out from the bottom of the beta-propeller structure abolishes binding of Nrf2. The structure of the Kelch domain of Keap1 represents a high quality model for the superfamily of eukaryotic kelch repeat proteins and provides insight into how disease-causing mutations perturb the structural integrity of the Kelch domain.


  • Organizational Affiliation
    • Department of Biochemistry, University of Misouri-Columbia, Misouri 65211, USA.

Macromolecule Content 

  • Total Structure Weight: 33.69 kDa 
  • Atom Count: 2,527 
  • Modeled Residue Count: 288 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
kelch-like ECH-associated protein 1A [auth X]308Homo sapiensMutation(s): 0 
Gene Names: Keap1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
PHAROS:  Q14145
GTEx:  ENSG00000079999 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14145
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.182 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.148 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.892α = 90
b = 85.892β = 90
c = 148.753γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations