2VPE

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Decoding of Methylated Histone H3 Tail by the Pygo- Bcl9 Wnt Signaling Complex.

Fiedler, M.Sanchez-Barrena, M.J.Nekrasov, M.Mieszczanek, J.Rybin, V.Muller, J.Evans, P.Bienz, M.

(2008) Mol.Cell 30: 507

  • DOI: 10.1016/j.molcel.2008.03.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pygo and BCL9/Legless transduce the Wnt signal by promoting the transcriptional activity of beta-catenin/Armadillo in normal and malignant cells. We show that human and Drosophila Pygo PHD fingers associate with their cognate HD1 domains from BCL9/Le ...

    Pygo and BCL9/Legless transduce the Wnt signal by promoting the transcriptional activity of beta-catenin/Armadillo in normal and malignant cells. We show that human and Drosophila Pygo PHD fingers associate with their cognate HD1 domains from BCL9/Legless to bind specifically to the histone H3 tail methylated at lysine 4 (H3K4me). The crystal structures of ternary complexes between PHD, HD1, and two different H3K4me peptides reveal a unique mode of histone tail recognition: efficient histone binding requires HD1 association, and the PHD-HD1 complex binds preferentially to H3K4me2 while displaying insensitivity to methylation of H3R2. Therefore, this is a prime example of histone tail binding by a PHD finger (of Pygo) being modulated by a cofactor (BCL9/Legless). Rescue experiments in Drosophila indicate that Wnt signaling outputs depend on histone decoding. The specificity of this process provided by the Pygo-BCL9/Legless complex suggests that this complex facilitates an early step in the transition from gene silence to Wnt-induced transcription.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYGOPUS HOMOLOG 1
A, C
63Homo sapiensMutation(s): 0 
Gene Names: PYGO1
Find proteins for Q9Y3Y4 (Homo sapiens)
Go to Gene View: PYGO1
Go to UniProtKB:  Q9Y3Y4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
B-CELL CLL/LYMPHOMA 9 PROTEIN
B, D
32Homo sapiensMutation(s): 0 
Gene Names: BCL9
Find proteins for O00512 (Homo sapiens)
Go to Gene View: BCL9
Go to UniProtKB:  O00512
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3 TAIL
P, R
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
P, R
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.720α = 90.00
b = 105.720β = 90.00
c = 51.430γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance