5HQ2 Transferase Dna date Jan 21, 2016
title Structural Model Of Set8 Histone H4 Lys20 Methyltransferase Nucleosome Core Particle
authors G.Tavarekere, R.K.Mcginty, S.Tan
compound source
Molecule: Histone H3.2
Chain: A
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Pet3d

Molecule: Histone H4
Chain: B
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Pet3a

Molecule: Histone H2a
Chain: G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Pet3a

Molecule: Histone H2b 1.1
Chain: H
Synonym: H2b1.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Pet3a

Molecule: Dna (149-Mer)
Chain: I
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Gene: Widom 601 Nucleosome Positioning Sequence
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_plasmid: Plasmid

Molecule: Dna (149-Mer)
Chain: J
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Gene: Widom 601 Nucleosome Positioning Sequence
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_plasmid: Plasmid

Molecule: Guanine Nucleotide Exchange Factor Srm1
Chain: K
Synonym: Pheromone Response Pathway Component Srm1,Pre-Mrna Processing Protein 20,Regulator Of Chromosome Condensation, Of Receptor Mutations 1,Mrna Transport Protein 1;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Srm1, Mtr1, Prp20, Ygl097w
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Pst50tr

Molecule: N-Lysine Methyltransferase Setd8
Chain: M
Synonym: H4-K20-Hmtase Setd8,Histone-Lysine N-Methyltransfe Setd8,Lysine N-Methyltransferase 5a,Prset Domain-Containin 07,Prset07,Set Domain-Containing Protein 8;
Ec: 2.1.1.-,2.1.1.43
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Setd8, Kmt5a, Prset7, Set07, Set8
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Pst50tr
symmetry Space Group: C 2 2 21
R_factor 0.339 R_Free 0.397
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.729 300.752 182.090 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.50 Å
ligand
enzyme Transferase E.C.2.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


G


H


K


M


Primary referenceMultivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate., Girish TS, McGinty RK, Tan S, J Mol Biol. 2016 Apr 24;428(8):1531-43. doi: 10.1016/j.jmb.2016.02.025. Epub 2016, Mar 4. PMID:26953260
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (168 Kb) [Save to disk]
  • Biological Unit Coordinates (5hq2.pdb1.gz) 309 Kb
  • CSU: Contacts of Structural Units for 5HQ2
  • Structure Factors (352 Kb)
  • Retrieve 5HQ2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HQ2 from S2C, [Save to disk]
  • Re-refined 5hq2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5HQ2 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 5HQ2
  • 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: [5hq2] [5hq2_G] [5hq2_A] [5hq2_I] [5hq2_K] [5hq2_J] [5hq2_M] [5hq2_H] [5hq2_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5HQ2: [H2A] [H2B] [H3] [H4] [SET ] by SMART
  • Other resources with information on 5HQ2
  • Community annotation for 5HQ2 at PDBWiki (http://pdbwiki.org)

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