3W96 Structural Protein Dna date Apr 01, 2013
title Crystal Structure Of Human Nucleosome Core Particle Lacking Terminal Region
authors W.Iwasaki, Y.Miya, N.Horikoshi, A.Osakabe, H.Tachiwana, T.Shibata W.Kagawa, H.Kurumizaka
compound source
Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a, Histone H3b, Histone H3c, Histone Histone H3f, Histone H3h, Histone H3i, Histone H3j, His Histone 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
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

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 Type 1-Be
Chain: C, G
Fragment: Unp Residues 11-130
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_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

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
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: 146-Mer Dna
Chain: I, J
Engineered: Yes

Synthetic: Yes
Other_details: Palindromic 146-Bp Human Alpha-Satellite Rep
symmetry Space Group: P 21 21 21
R_factor 0.247 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.515 109.319 175.658 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceContribution of histone N-terminal tails to the structure and stability of nucleosomes., Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H, FEBS Open Bio. 2013 Aug 22;3:363-9. doi: 10.1016/j.fob.2013.08.007. PMID:24251097
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (246 Kb) [Save to disk]
  • Biological Unit Coordinates (3w96.pdb1.gz) 239 Kb
  • LPC: Ligand-Protein Contacts for 3W96
  • CSU: Contacts of Structural Units for 3W96
  • Structure Factors (329 Kb)
  • Retrieve 3W96 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3W96 from S2C, [Save to disk]
  • Re-refined 3w96 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3W96 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 3W96
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3W96, from MSDmotif at EBI
  • Fold representative 3w96 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3w96_A] [3w96] [3w96_J] [3w96_E] [3w96_B] [3w96_C] [3w96_D] [3w96_H] [3w96_F] [3w96_G] [3w96_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3W96: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3W96
  • Community annotation for 3W96 at PDBWiki (http://pdbwiki.org)

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