2X4Y Transcription date Feb 02, 2010
title Molecular Basis Of Histone H3k36me3 Recognition By The Pwwp Brpf1.
authors A.Vezzoli, N.Bonadies, M.D.Allen, S.M.V.Freund, C.M.Santiveri, B. B.J.P.Huntly, B.Gottgens, M.Bycroft
compound source
Molecule: Peregrin
Chain: A, C, E, G, I, K, M, O
Fragment: Brpf1 Pwwp Domain, Residues 1076-1205
Synonym: Bromodomain And Phd Finger-Containing Protein 1, P Br140;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: C41
Expression_system_vector: Prseta

Molecule: Histone H3.2
Chain: B, D, F, H, J, L, N, P
Fragment: Residues 23-43
Synonym: Human H3 Histone, H3m, H3o
Engineered: Yes
Other_details: Trimethylated At Position 36

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor 0.190 R_Free 0.227
length a length b length c angle alpha angle beta angle gamma
35.757 97.906 102.524 86.80 80.96 87.24
method X-Ray Diffractionresolution 1.70 Å
ligand M3L, SO4 enzyme
Primary referenceMolecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1., Vezzoli A, Bonadies N, Allen MD, Freund SM, Santiveri CM, Kvinlaug BT, Huntly BJ, Gottgens B, Bycroft M, Nat Struct Mol Biol. 2010 Apr 18. PMID:20400950
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (211 Kb) [Save to disk]
  • Biological Unit Coordinates (2x4y.pdb1.gz) 26 Kb
  • Biological Unit Coordinates (2x4y.pdb2.gz) 30 Kb
  • Biological Unit Coordinates (2x4y.pdb3.gz) 28 Kb
  • Biological Unit Coordinates (2x4y.pdb4.gz) 28 Kb
  • Biological Unit Coordinates (2x4y.pdb5.gz) 28 Kb
  • Biological Unit Coordinates (2x4y.pdb6.gz) 28 Kb
  • Biological Unit Coordinates (2x4y.pdb7.gz) 27 Kb
  • Biological Unit Coordinates (2x4y.pdb8.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 2X4Y
  • CSU: Contacts of Structural Units for 2X4Y
  • Structure Factors (976 Kb)
  • Retrieve 2X4Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X4Y from S2C, [Save to disk]
  • Re-refined 2x4y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2X4Y 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 2X4Y
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2X4Y, from MSDmotif at EBI
  • Fold representative 2x4y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x4y_E] [2x4y_F] [2x4y_K] [2x4y_B] [2x4y_M] [2x4y] [2x4y_A] [2x4y_L] [2x4y_H] [2x4y_D] [2x4y_N] [2x4y_J] [2x4y_P] [2x4y_G] [2x4y_O] [2x4y_C] [2x4y_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2X4Y: [PWWP ] by SMART
  • Other resources with information on 2X4Y
  • Community annotation for 2X4Y 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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