3HQM | pdb_00003hqm

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.218 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3HQM

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 35.97 kDa 
  • Atom Count: 2,712 
  • Modeled Residue Count: 281 
  • Deposited Residue Count: 314 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Speckle-type POZ protein
A, B
145Homo 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
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein cubitus interruptus
C, D
12Drosophila melanogasterMutation(s): 0 
Gene Names: ci
UniProt
Find proteins for P19538 (Drosophila melanogaster)
Explore P19538 
Go to UniProtKB:  P19538
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19538
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.218 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.281α = 63
b = 48.1β = 64.04
c = 49.86γ = 62.89
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
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: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description