3HSV

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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: 10.1016/j.molcel.2009.09.022
  • Structures With Same Primary Citation

  • 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 defi ...

    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: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Core histone macro-H2A.1
M
16Homo sapiensMutation(s): 0 
Gene Names: MACROH2A1H2AFY
Find proteins for O75367 (Homo sapiens)
Go to UniProtKB:  O75367
NIH Common Fund Data Resources
PHAROS  O75367
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Speckle-type POZ protein
A, B
145Homo sapiensMutation(s): 1 
Gene Names: SPOP
Find proteins for Q5NVK7 (Pongo abelii)
Go to UniProtKB:  Q5NVK7
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.953α = 90
b = 43.086β = 118.15
c = 87.453γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-19
    Changes: Advisory, Database references, Derived calculations, Source and taxonomy, Structure summary