5B31 Dna Binding Protein date Feb 08, 2016
title The Crystal Structure Of The Heterotypic H2azh2a Nucleosome H3.1.
authors N.Horikoshi, H.Taguchi, Y.Arimura, 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: Ph3.1

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)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph4

Molecule: Histone H2a Type 1-Be
Chain: C
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: Ph2a

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: Ph2b

Molecule: Histone H2a.Z
Chain: G
Synonym: H2az
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2afz, H2az
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph2a.Z.1

Molecule: Dna (146-Mer)
Chain: I, J
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T Easy
symmetry Space Group: P 21 21 21
R_factor 0.225 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.110 109.685 181.487 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C


F, B


G


H, D


Primary referenceCrystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A., Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H, Open Biol. 2016 Jun;6(6). pii: 160127. doi: 10.1098/rsob.160127. PMID:27358293
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (250 Kb) [Save to disk]
  • Biological Unit Coordinates (5b31.pdb1.gz) 242 Kb
  • LPC: Ligand-Protein Contacts for 5B31
  • CSU: Contacts of Structural Units for 5B31
  • Structure Factors (1677 Kb)
  • Retrieve 5B31 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B31 from S2C, [Save to disk]
  • Re-refined 5b31 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5B31 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 5B31
  • 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: [5b31_F] [5b31_D] [5b31_A] [5b31_H] [5b31_J] [5b31_I] [5b31_B] [5b31] [5b31_G] [5b31_C] [5b31_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5B31: [H2A] [H2B] [H3] [H4 ] by SMART
    • Other resources with information on 5B31
  • Community annotation for 5B31 at PDBWiki (http://pdbwiki.org)

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