2VPJ

Crystal structure of the Kelch domain of human KLHL12

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structural Basis for Cul3 Assembly with the Btb-Kelch Family of E3 Ubiquitin Ligases.

Canning, P., Cooper, C.D.O., Krojer, T., Murray, J.W., Pike, A.C.W., Chaikuad, A., Keates, T., Thangaratnarajah, C., Hojzan, V., Marsden, B.D., Gileadi, O., Knapp, S., von Delft, F., Bullock, A.N.

(2013) J Biol Chem 288: 7803

  • DOI: 10.1074/jbc.M112.437996
  • Primary Citation of Related Structures:  
    2VPJ, 4ASC, 2XN4, 4AP2, 4APF, 3II7

  • PubMed Abstract: 

    • Cullin-RING ligases are multisubunit E3 ubiquitin ligases that recruit substrate-specific adaptors to catalyze protein ubiquitylation. Cul3-based Cullin-RING ligases are uniquely associated with BTB adaptors that incorporate homodimerization, Cul3 assembly, and substrate recognition into a single multidomain protein, of which the best known are BTB-BACK-Kelch domain proteins, including KEAP1 ...

    Cullin-RING ligases are multisubunit E3 ubiquitin ligases that recruit substrate-specific adaptors to catalyze protein ubiquitylation. Cul3-based Cullin-RING ligases are uniquely associated with BTB adaptors that incorporate homodimerization, Cul3 assembly, and substrate recognition into a single multidomain protein, of which the best known are BTB-BACK-Kelch domain proteins, including KEAP1. Cul3 assembly requires a BTB protein "3-box" motif, analogous to the F-box and SOCS box motifs of other Cullin-based E3s. To define the molecular basis for this assembly and the overall architecture of the E3, we determined the crystal structures of the BTB-BACK domains of KLHL11 both alone and in complex with Cul3, along with the Kelch domain structures of KLHL2 (Mayven), KLHL7, KLHL12, and KBTBD5. We show that Cul3 interaction is dependent on a unique N-terminal extension sequence that packs against the 3-box in a hydrophobic groove centrally located between the BTB and BACK domains. Deletion of this N-terminal region results in a 30-fold loss in affinity. The presented data offer a model for the quaternary assembly of this E3 class that supports the bivalent capture of Nrf2 and reveals potential new sites for E3 inhibitor design.

    Organizational Affiliation: 

    Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KELCH-LIKE PROTEIN 12A301Homo sapiensMutation(s): 0 
Gene Names: KLHL12, C3IP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q53G59 (Homo sapiens)
Explore Q53G59 
Go to UniProtKB:  Q53G59
PHAROS:  Q53G59
GTEx:  ENSG00000117153
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download Ideal Coordinates CCD File 
 B [auth A], C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.637α = 90
b = 61.546β = 111.75
c = 45.523γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-02-06
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2013-03-27
    Changes: Database references
  • Version 1.4: 2018-01-24
    Changes: Database references