3F9Z Transferase date Nov 14, 2008
title Structural Insights Into Lysine Multiple Methylation By Set Methyltransferases, Set8-Y245f H4-Lys20 Adohcy
authors J.F.Couture, L.M.A.Dirk, J.S.Brunzelle, R.L.Houtz, R.C.Trievel
compound source
Molecule: Histone-Lysine N-Methyltransferase Setd8
Chain: A, B, C, D
Fragment: Set Domain: Unp Residues 232-393
Synonym: H4-K20-Hmtase Setd8, Set Domain-Containing Protein Domain-Containing Protein 07, Prset07, Pr-Set7, Lysine N- Methyltransferase 5a;
Ec: 2.1.1.43
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Setd8, Kmt5a, Prset7, Set07, Set8
Expression_system: Escherichia Coli
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_vector: Parallel
Expression_system_plasmid: Phis2

Molecule: Histone H4
Chain: E, F, G, H
Fragment: Unp Residues 16-25
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Corresponding To Residues Human Histone H4
symmetry Space Group: P 1
R_factor 0.216 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.990 45.550 94.410 89.37 87.09 90.50
method X-Ray Diffractionresolution 1.60 Å
ligand SAH enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural origins for the product specificity of SET domain protein methyltransferases., Couture JF, Dirk LM, Brunzelle JS, Houtz RL, Trievel RC, Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20659-64. Epub 2008 Dec 16. PMID:19088188
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (137 Kb) [Save to disk]
  • Biological Unit Coordinates (3f9z.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (3f9z.pdb2.gz) 34 Kb
  • Biological Unit Coordinates (3f9z.pdb3.gz) 33 Kb
  • Biological Unit Coordinates (3f9z.pdb4.gz) 34 Kb
  • LPC: Ligand-Protein Contacts for 3F9Z
  • CSU: Contacts of Structural Units for 3F9Z
  • Likely Quarternary Molecular Structure file(s) for 3F9Z
  • Structure Factors (1367 Kb)
  • Retrieve 3F9Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F9Z from S2C, [Save to disk]
  • Re-refined 3f9z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F9Z 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 3F9Z
  • 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 3F9Z, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f9z_G] [3f9z_D] [3f9z] [3f9z_C] [3f9z_F] [3f9z_E] [3f9z_H] [3f9z_B] [3f9z_A]
  • SWISS-PROT database: [P62805] [Q9NQR1]
  • Domain organization of [H4_HUMAN] [SETD8_HUMAN] by SWISSPFAM
  • Domain found in 3F9Z: [SET ] by SMART
  • Other resources with information on 3F9Z
  • Community annotation for 3F9Z 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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