5Z30 Dna Binding Protein Dna date Jan 05, 2018
title The Crystal Structure Of The Nucleosome Containing A Cancer- Histone H2a.Z R80c Mutant
authors N.Horikoshi, 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_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)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H2a.Z
Chain: C, G
Synonym: H2az
Engineered: Yes
Mutation: 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: 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 (146-Mer)
Chain: I, J
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli Dh5alpha
Expression_system_taxid: 668369
Expression_system_strain: Dh5alpha
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T-Easy
symmetry Space Group: P 21 21 21
R_factor 0.202 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.399 108.332 170.902 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceCancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome., Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H, Nucleic Acids Res. 2018 Jul 24. pii: 5057090. doi: 10.1093/nar/gky661. PMID:30053102
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (244 Kb) [Save to disk]
  • Biological Unit Coordinates (5z30.pdb1.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 5Z30
  • CSU: Contacts of Structural Units for 5Z30
  • Structure Factors (2275 Kb)
  • Retrieve 5Z30 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Z30 from S2C, [Save to disk]
    • View 5Z30 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 5Z30
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5z30_B] [5z30_I] [5z30_G] [5z30_C] [5z30_E] [5z30_H] [5z30_D] [5z30_J] [5z30_A] [5z30_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5Z30
  • Community annotation for 5Z30 at PDBWiki (http://pdbwiki.org)

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