5Y0C Dna Binding Protein Dna date Jul 16, 2017
title Crystal Structure Of The Human Nucleosome At 2.09 Angstrom R
authors H.Kurumizaka, Y.Arimura, R.Fujita, M.Noda
compound source
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_vector_type: Plasmid

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: 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_cell: Jm109(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph4

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
Expression_system_taxid: 562
Expression_system_cell: 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_vector_type: Plasmid
Expression_system_plasmid: Ph2b
symmetry Space Group: P 21 21 21
R_factor 0.202 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.913 107.103 167.003 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.09 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] (255 Kb) [Save to disk]
  • Biological Unit Coordinates (5y0c.pdb1.gz) 247 Kb
  • LPC: Ligand-Protein Contacts for 5Y0C
  • CSU: Contacts of Structural Units for 5Y0C
  • Structure Factors (2577 Kb)
  • Retrieve 5Y0C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y0C from S2C, [Save to disk]
  • View 5Y0C 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 5Y0C
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5y0c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5y0c_H] [5y0c_F] [5y0c_E] [5y0c_G] [5y0c_C] [5y0c_B] [5y0c_D] [5y0c_I] [5y0c_A] [5y0c_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Y0C
  • Community annotation for 5Y0C at PDBWiki (http://pdbwiki.org)

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