5JRG Dna Binding Protein Dna date May 06, 2016
title Crystal Structure Of The Nucleosome Containing The Dna With Tetrahydrofuran (Thf)
authors A.Osakabe, Y.Arimura, N.Horikoshi, H.Kurumizaka
compound source
Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a,Histone H3b,Histone H3c,Histone H3 H3f,Histone H3h,Histone H3i,Histone H3j,Histone H3k,Hi H3l;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h3a, H3fa, Hist1h3b, H3fl, Hist1h3c, H3fc, Hist1 H3fb, Hist1h3e, H3fd, Hist1h3f, H3fi, Hist1h3g, H3fh, Hist1 H3fk, Hist1h3i, H3ff, Hist1h3j, H3fj;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H4
Chain: B, F
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a, H4a, H4fa, Hist1h4b, H4i, H4fi, Hist1h4c, H4fg, Hist1h4d, H4b, H4fb, Hist1h4e, H4j, H4fj, Hist1h4f, H4fc, Hist1h4h, H4h, H4fh, Hist1h4i, H4m, H4fm, Hist1h4j, H4fe, Hist1h4k, H4d, H4fd, Hist1h4l, H4k, H4fk, Hist2h4a, H4f2, H4fn, Hist2h4, Hist2h4b, H4o, H4fo, Hist4h4;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109(De3)

Molecule: Histone H2a Type 1-Be
Chain: C, G
Synonym: Histone H2a.2,Histone H2aa,Histone H2am
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ab, H2afm, Hist1h2ae, H2afa
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H2b Type 1-J
Chain: D, H
Synonym: Histone H2b.1,Histone H2b.R,H2br
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bj, H2bfr
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Dna (145-Mer)
Chain: I
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli Dh5alpha
Expression_system_taxid: 668369
Expression_system_strain: Dh5a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T Easy

Molecule: Dna (145-Mer)
Chain: J
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli Dh5alpha
Expression_system_taxid: 668369
Expression_system_strain: Dh5a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T Easy
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.491 108.773 169.571 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 3DR, CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referencePolymorphism of apyrimidinic DNA structures in the nucleosome., Osakabe A, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H, Sci Rep. 2017 Jan 31;7:41783. doi: 10.1038/srep41783. PMID:28139742
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (251 Kb) [Save to disk]
  • Biological Unit Coordinates (5jrg.pdb1.gz) 243 Kb
  • LPC: Ligand-Protein Contacts for 5JRG
  • CSU: Contacts of Structural Units for 5JRG
  • Structure Factors (920 Kb)
  • Retrieve 5JRG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JRG from S2C, [Save to disk]
  • Re-refined 5jrg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JRG 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 5JRG
  • 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: [5jrg_D] [5jrg_B] [5jrg] [5jrg_C] [5jrg_A] [5jrg_E] [5jrg_F] [5jrg_G] [5jrg_I] [5jrg_H] [5jrg_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5JRG
  • Community annotation for 5JRG at PDBWiki (http://pdbwiki.org)

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