3HVE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.302 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gigaxonin256Homo sapiensMutation(s): 0 
Gene Names: GANGAN1KLHL16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2C0 (Homo sapiens)
Explore Q9H2C0 
Go to UniProtKB:  Q9H2C0
PHAROS:  Q9H2C0
GTEx:  ENSG00000261609 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2C0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gigaxonin256Homo sapiensMutation(s): 0 
Gene Names: GANGAN1KLHL16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2C0 (Homo sapiens)
Explore Q9H2C0 
Go to UniProtKB:  Q9H2C0
PHAROS:  Q9H2C0
GTEx:  ENSG00000261609 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2C0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.302 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.48α = 90
b = 55.6β = 91.1
c = 120.6γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
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: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-06-27
    Changes: Data collection