3F9W	Transferase	date	Nov 14, 2008
title	Structural Insights Into Lysine Multiple Methylation By Set Domain Methyltransferases, Set8-Y334f 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 8, Prset 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 16-25 Of Human Histone H4
symmetry	Space Group: P 1	R_factor 0.162 R_Free 0.206
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.000 45.600 94.200 89.20 87.10 90.80
method	X-Ray Diffraction	resolution	1.60 Å
ligand	SAH	enzyme	Transferase E.C.2.1.1.43 BRENDA
Gene Ontology	Chain Function Process Component H, F, G, E DNA binding protein binding protein heterodimerization a... telomere maintenance chromatin organization nucleosome assembly CENP-A containing nucleosome... negative regulation of megak... phosphatidylinositol-mediate... nucleosome extracellular region nucleus nucleoplasm chromosome nucleolus actin cytoskeleton
Primary reference	Structural 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] (266 Kb) [Save to disk] Biological Unit Coordinates (3f9w.pdb1.gz) 66 Kb Biological Unit Coordinates (3f9w.pdb2.gz) 67 Kb Biological Unit Coordinates (3f9w.pdb3.gz) 68 Kb Biological Unit Coordinates (3f9w.pdb4.gz) 68 Kb LPC: Ligand-Protein Contacts for 3F9W CSU: Contacts of Structural Units for 3F9W Likely Quarternary Molecular Structure file(s) for 3F9W Structure Factors (1368 Kb) Retrieve 3F9W in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3F9W from S2C, [Save to disk] Re-refined 3f9w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3F9W 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3F9W

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 3F9W, from MSDmotif at EBI Fold representative 3f9w from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3f9w_A] [3f9w_B] [3f9w_C] [3f9w_D] [3f9w_E] [3f9w_F] [3f9w_G] [3f9w_H] SWISS-PROT database: [P62805] [Q9NQR1] Domain organization of [H4_HUMAN] [SETD8_HUMAN] by SWISSPFAM Domain found in 3F9W: [SET ] by SMART Alignments of the sequence of 3F9W with the sequences similar proteins can be viewed for 3F9W's classification [H4_HUMAN] [SETD8_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [H4_HUMAN] [SETD8_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3F9W

Community annotation for 3F9W at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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