Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.240 

wwPDB Validation   3D Report Full Report

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Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases.

Zhuang, M.Calabrese, M.F.Liu, J.Waddell, M.B.Nourse, A.Hammel, M.Miller, D.J.Walden, H.Duda, D.M.Seyedin, S.N.Hoggard, T.Harper, J.W.White, K.P.Schulman, B.A.

(2009) Mol Cell 36: 39-50

  • DOI: https://doi.org/10.1016/j.molcel.2009.09.022
  • Primary Citation of Related Structures:  
    3HQH, 3HQI, 3HQL, 3HQM, 3HSV, 3HTM, 3HU6, 3HVE, 3IVQ, 3IVV

  • PubMed Abstract: 

    In the largest E3 ligase subfamily, Cul3 binds a BTB domain, and an associated protein-interaction domain such as MATH recruits substrates for ubiquitination. Here, we present biochemical and structural analyses of the MATH-BTB protein, SPOP. We define a SPOP-binding consensus (SBC) and determine structures revealing recognition of SBCs from the phosphatase Puc, the transcriptional regulator Ci, and the chromatin component MacroH2A. We identify a dimeric SPOP-Cul3 assembly involving a conserved helical structure C-terminal of BTB domains, which we call "3-box" due to its facilitating Cul3 binding and its resemblance to F-/SOCS-boxes in other cullin-based E3s. Structural flexibility between the substrate-binding MATH and Cul3-binding BTB/3-box domains potentially allows a SPOP dimer to engage multiple SBCs found within a single substrate, such as Puc. These studies provide a molecular understanding of how MATH-BTB proteins recruit substrates to Cul3 and how their dimerization and conformational variability may facilitate avid interactions with diverse substrates.

  • Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Speckle-type POZ protein
A, B
312Homo sapiensMutation(s): 1 
Gene Names: SPOP
UniProt & NIH Common Fund Data Resources
Find proteins for O43791 (Homo sapiens)
Explore O43791 
Go to UniProtKB:  O43791
PHAROS:  O43791
GTEx:  ENSG00000121067 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43791
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C, D
7Drosophila melanogasterMutation(s): 0 
Gene Names: puc
EC: 3.1.3 (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for Q9VHV8 (Drosophila melanogaster)
Explore Q9VHV8 
Go to UniProtKB:  Q9VHV8
Entity Groups  
UniProt GroupQ9VHV8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.74α = 90
b = 107.74β = 90
c = 130.79γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description