3ZPV

Crystal structure of Drosophila Pygo PHD finger in complex with Legless HD1 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Evolutionary Adaptation of the Fly Pygo Phd Finger Towards Recognizing Histone H3 Tail Methylated at Arginine 2

Miller, T.C.R.Mieszczanek, J.Sanchez-Barrena, M.J.Rutherford, T.J.Fiedler, M.Bienz, M.

(2013) Structure 21: 2208

  • DOI: https://doi.org/10.1016/j.str.2013.09.013
  • Primary Citation of Related Structures:  
    3ZPV

  • PubMed Abstract: 

    Pygo proteins promote Armadillo- and β-catenin-dependent transcription, by relieving Groucho-dependent repression of Wnt targets. Their PHD fingers bind histone H3 tail methylated at lysine 4, and to the HD1 domain of their Legless/BCL9 cofactors, linking Pygo to Armadillo/β-catenin. Intriguingly, fly Pygo orthologs exhibit a tryptophan > phenylalanine substitution in their histone pocket-divider which reduces their affinity for histones. Here, we use X-ray crystallography and NMR, to discover a conspicuous groove bordering this phenylalanine in the Drosophila PHD-HD1 complex--a semi-aromatic cage recognizing asymmetrically methylated arginine 2 (R2me2a), a chromatin mark of silenced genes. Our structural model of the ternary complex reveals a distinct mode of dimethylarginine recognition, involving a polar interaction between R2me2a and its groove, the structural integrity of which is crucial for normal tissue patterning. Notably, humanized fly Pygo derepresses Notch targets, implying an inherent Notch-related function of classical Pygo orthologs, disabled in fly Pygo, which thus appears dedicated to Wnt signaling.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN BCL9 HOMOLOG37Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for Q961D9 (Drosophila melanogaster)
Explore Q961D9 
Go to UniProtKB:  Q961D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ961D9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN PYGOPUS62Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for Q9V9W8 (Drosophila melanogaster)
Explore Q9V9W8 
Go to UniProtKB:  Q9V9W8
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UniProt GroupQ9V9W8
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN PYGOPUSIA [auth Y],
O [auth E],
Y [auth O]
62Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for Q9V9W8 (Drosophila melanogaster)
Explore Q9V9W8 
Go to UniProtKB:  Q9V9W8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V9W8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth G]
BB [auth G]
CB [auth I]
DB [auth I]
EB [auth K]
AB [auth G],
BB [auth G],
CB [auth I],
DB [auth I],
EB [auth K],
FB [auth K],
GB [auth M],
HB [auth M],
IB [auth O],
JB [auth O],
KA [auth 1],
KB [auth Q],
LA [auth 1],
LB [auth Q],
MA [auth 3],
MB [auth S],
NA [auth 3],
NB [auth S],
OA [auth 5],
OB [auth U],
PA [auth 5],
PB [auth U],
QA [auth 7],
QB [auth W],
RA [auth 7],
RB [auth W],
SA [auth 9],
SB [auth Y],
TA [auth 9],
TB [auth Y],
UA [auth A],
VA [auth A],
WA [auth C],
XA [auth C],
YA [auth E],
ZA [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.21α = 90
b = 111.96β = 90
c = 190.76γ = 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: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-11-13
    Changes: Database references
  • Version 1.2: 2013-12-25
    Changes: Database references
  • Version 1.3: 2014-02-19
    Changes: Atomic model, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description