2VPD	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, P.Evans, M.Bienz
compound		source
Molecule: Pygopus Homolog 1 Chain: A, C Fragment: Phd Domain, Residues 333-398 Synonym: Hpygo1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_variant: Codonplus(De3)-Ril Expression_system_vector: Bi-Cistronic Expression Vector
Molecule: B-Cell Clllymphoma 9 Protein Chain: B, D Fragment: Hd1 Domain, Residues 174-205 Synonym: Bcl9, B-Cell Lymphoma 9 Protein, Protein Legless H Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_variant: Codonplus(De3)-Ril Expression_system_vector: Bi-Cistronic Expression Vector
symmetry	Space Group: C 2 2 21	R_factor 0.234 R_Free 0.267
crystal cell	length a length b length c angle alpha angle beta angle gamma 88.720 100.890 64.240 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.77 Å
ligand	ZN	enzyme
Gene Ontology	Chain Function Process Component D, B
Primary reference	Decoding 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] (35 Kb) [Save to disk] Biological Unit Coordinates (2vpd.pdb1.gz) 15 Kb Biological Unit Coordinates (2vpd.pdb2.gz) 16 Kb LPC: Ligand-Protein Contacts for 2VPD CSU: Contacts of Structural Units for 2VPD Likely Quarternary Molecular Structure file(s) for 2VPD Structure Factors (84 Kb) Retrieve 2VPD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VPD from S2C, [Save to disk] Re-refined 2vpd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VPD 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 2VPD

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 2VPD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vpd_C] [2vpd_D] [2vpd_B] [2vpd] [2vpd_A] SWISS-PROT database: [O00512] [Q9Y3Y4] Domain organization of [BCL9_HUMAN] [PYGO1_HUMAN] by SWISSPFAM Domain found in 2VPD: [PHD ] by SMART

Other resources with information on 2VPD

Community annotation for 2VPD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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