5CIU Transferase date Jul 13, 2015
title Structural Basis Of The Recognition Of H3k36me3 By Dnmt3b Pw
authors G.Rondelet, T.Dal Maso, L.Willems, J.Wouters
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 3b
Chain: A, B
Synonym: Dnmt3b,Dna Methyltransferase Hsaiiib,M.Hsaiiib
Ec: 2.1.1.37
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3b
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl

Molecule: Histone H3.2
Chain: C, D
Synonym: Histone H3m,Histone H3o
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 32 2 1
R_factor 0.224 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.437 73.437 158.200 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.24 Å
ligand GOL, M3L enzyme Transferase E.C.2.1.1.37 BRENDA
Primary referenceStructural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B., Rondelet G, Dal Maso T, Willems L, Wouters J, J Struct Biol. 2016 Jun;194(3):357-67. doi: 10.1016/j.jsb.2016.03.013. Epub 2016 , Mar 15. PMID:26993463
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (5ciu.pdb1.gz) 25 Kb
  • Biological Unit Coordinates (5ciu.pdb2.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 5CIU
  • CSU: Contacts of Structural Units for 5CIU
  • Structure Factors (420 Kb)
  • Retrieve 5CIU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CIU from S2C, [Save to disk]
  • Re-refined 5ciu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CIU 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 5CIU
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ciu_C] [5ciu_D] [5ciu_B] [5ciu_A] [5ciu]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5CIU: [PWWP ] by SMART
  • Other resources with information on 5CIU
  • Community annotation for 5CIU at PDBWiki (http://pdbwiki.org)

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