2VPG Gene Regulation date Feb 27, 2008
title Decoding Of Methylated Histone H3 Tail By The Pygo-Bcl9 Wnt Complex
authors M.Fiedler, M.J.Sanchez-Barrena, M.Nekrasov, J.Mieszczanek, V.Ryb J.Muller, M.Bienz, P.Evans
compound source
Molecule: Pygopus Homolog 1
Chain: A, C
Fragment: Phd Domain, Residues 340-398
Synonym: Hpygo1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codonplus-Ril
Expression_system_vector: Bi-Cistronic Expression Vector

Molecule: B-Cell Clllymphoma 9 Protein
Chain: B, D
Fragment: Hd1 Domain, Residues 177-205
Synonym: B-Cell Lymphoma 9 Protein, Bcl-9, Protein Legless Bcl9;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codonplus-Ril
Expression_system_vector: Bi-Cistronic Expression Vector

Molecule: Histone H3 Tail
Chain: P, R
Engineered: Yes
Other_details: 18-Mer H3r2me2ak4me2, Dimethylation At Lys K Asymmetric Dimethylation At R2

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 4 21 2
R_factor 0.201 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.750 105.750 51.420 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand DA2, GOL, MLY, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
D, B


R, P


Primary referenceDecoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex., Fiedler M, Sanchez-Barrena MJ, Nekrasov M, Mieszczanek J, Rybin V, Muller J, Evans P, Bienz M, Mol Cell. 2008 May 23;30(4):507-18. PMID:18498752
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (2vpg.pdb1.gz) 19 Kb
  • Biological Unit Coordinates (2vpg.pdb2.gz) 19 Kb
  • LPC: Ligand-Protein Contacts for 2VPG
  • CSU: Contacts of Structural Units for 2VPG
  • Likely Quarternary Molecular Structure file(s) for 2VPG
  • Structure Factors (457 Kb)
  • Retrieve 2VPG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VPG from S2C, [Save to disk]
  • Re-refined 2vpg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VPG in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2VPG
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2VPG, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vpg] [2vpg_R] [2vpg_C] [2vpg_D] [2vpg_B] [2vpg_A] [2vpg_P]
  • SWISS-PROT database: [O00512] [Q9Y3Y4]
  • Domain organization of [BCL9_HUMAN] [PYGO1_HUMAN] by SWISSPFAM
  • Domain found in 2VPG: [PHD ] by SMART
  • Other resources with information on 2VPG
  • Community annotation for 2VPG at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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