4Z5T The nucleosome containing human H3.5 date
authors Urahama, T., Harada, A., Maehara, K., Horikoshi, N., Sato, K., Sato, Y., Shiraishi, K., Sugino, N., Osakabe, A., Tachiwana, H., Kagawa, W., Kimura, H., Ohkawa, Y., Kurumizaka, H.
compound source
symmetry
R_factor
R_Free 0.2694
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceHistone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis., Urahama T, Harada A, Maehara K, Horikoshi N, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H, Epigenetics Chromatin. 2016 Jan 15;9:2. doi: 10.1186/s13072-016-0051-y., eCollection 2016. PMID:26779285
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (4z5t.pdb1.gz) 237 Kb
  • CSU: Contacts of Structural Units for 4Z5T
  • Structure Factors (770 Kb)
  • Retrieve 4Z5T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Z5T from S2C, [Save to disk]
  • Re-refined 4z5t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4Z5T 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 4Z5T
  • 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: [4z5t_J] [4z5t_C] [4z5t] [4z5t_H] [4z5t_I] [4z5t_A] [4z5t_E] [4z5t_F] [4z5t_B] [4z5t_D] [4z5t_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4Z5T: [H2A] [H2B] [H3] [H4 ] by SMART
    • Other resources with information on 4Z5T
  • Community annotation for 4Z5T at PDBWiki (http://pdbwiki.org)

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