2VPB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    2VPD, 2VPE, 2VPG, 2VPB, 2VP7

  • 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/Legless to bind specifically to the histone H3 tail methylated at lysine 4 (H3K4me) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYGOPUS HOMOLOG 1 A65Homo sapiensMutation(s): 0 
Gene Names: PYGO1
Find proteins for Q9Y3Y4 (Homo sapiens)
Explore Q9Y3Y4 
Go to UniProtKB:  Q9Y3Y4
NIH Common Fund Data Resources
PHAROS:  Q9Y3Y4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
B-CELL CLL/LYMPHOMA 9 PROTEIN B35Homo sapiensMutation(s): 0 
Gene Names: BCL9
Find proteins for O00512 (Homo sapiens)
Explore O00512 
Go to UniProtKB:  O00512
NIH Common Fund Data Resources
PHAROS:  O00512
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.1α = 90
b = 79.47β = 90
c = 91.83γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-29
    Changes: Data collection, Experimental preparation