2VPG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 2.1 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/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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYGOPUS HOMOLOG 1AC63Homo 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
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
B-CELL CLL/LYMPHOMA 9 PROTEINBD32Homo 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
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H3 TAILPR18Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DA2
Query on DA2
P,RL-PEPTIDE LINKINGC8 H18 N4 O2ARG
MLY
Query on MLY
P,RL-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.75α = 90
b = 105.75β = 90
c = 51.42γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance
  • Version 2.0: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other, Polymer sequence
  • Version 2.1: 2019-05-29
    Changes: Data collection, Experimental preparation