3OUX | pdb_00003oux

Structure of beta-catenin with phosphorylated Lef-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.264 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.198 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Biochemical and structural characterization of beta-catenin interactions with nonphosphorylated and CK2-phosphorylated Lef-1.

Sun, J.Weis, W.I.

(2011) J Mol Biology 405: 519-530

  • DOI: https://doi.org/10.1016/j.jmb.2010.11.010
  • Primary Citation Related Structures: 
    3OUW, 3OUX

  • PubMed Abstract: 

    In the Wnt/β-catenin signaling pathway, β-catenin activates target genes through its interactions with the T-cell factor/lymphoid enhancer-binding factor (TCF/Lef) family of transcription factors. The crystal structures of complexes between the β-catenin armadillo domain and the Lef-1 N-terminal domain show that the overall conformation and many of the interactions are similar to other published structures of TCFs bound to β-catenin. However, a second salt bridge in other TCF-β-catenin structures is absent in the structure of β-catenin-Lef-1 complex, indicating that this feature is not obligatory for β-catenin binding. Casein kinase II (CK2) has been shown to act as a positive regulator of Wnt signaling, and Lef-1 is a substrate of CK2. In vitro phosphorylation of purified Lef-1 was used to examine the effect of CK2 on the interaction of Lef-1 with β-catenin. Mass spectrometry data show that CK2 phosphorylation of Lef-1 N-terminal domain results in a single phosphorylation site at Ser40. Isothermal titration calorimetry revealed that β-catenin binds to nonphosphorylated or CK2-phosphorylated Lef-1 with the same affinity, which is consistent with the absence of phospho-Ser40 interactions in the crystal structure of phosphorylated Lef-1 N-terminal domain bound to β-catenin. These data indicate that the effect of CK2 on the Wnt/β-catenin pathway does not appear to be at the level of the Lef-1-β-catenin interaction.


  • Organizational Affiliation
    • Department of Structural Biology, Stanford University School of Medicine,Stanford, CA 94305-5126, USA.

Macromolecule Content 

  • Total Structure Weight: 66.01 kDa 
  • Atom Count: 4,164 
  • Modeled Residue Count: 550 
  • Deposited Residue Count: 607 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Catenin beta-1540Mus musculusMutation(s): 0 
Gene Names: Ctnnb1Catnb
UniProt & NIH Common Fund Data Resources
Find proteins for Q02248 (Mus musculus)
Explore Q02248 
Go to UniProtKB:  Q02248
IMPC:  MGI:88276
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02248
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lymphoid enhancer-binding factor 167Mus musculusMutation(s): 0 
Gene Names: Lef1Lef-1
UniProt & NIH Common Fund Data Resources
Find proteins for P27782 (Mus musculus)
Explore P27782 
Go to UniProtKB:  P27782
IMPC:  MGI:96770
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27782
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.264 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.56α = 90
b = 115.56β = 90
c = 195.93γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 1.3: 2015-12-09
    Changes: Other
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary