4Z5T Structural Protein Dna date Apr 03, 2015
title The Nucleosome Containing Human H3.5
authors T.Urahama, A.Harada, K.Maehara, N.Horikoshi, K.Sato, Y.Sato, K.Shi N.Sugino, A.Osakabe, H.Tachiwana, W.Kagawa, H.Kimura, Y.Ohkawa, H.Kurumizaka
compound source
Molecule: Histone H3.3c
Chain: A, E
Synonym: Histone H3.5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3f3c
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
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 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: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19

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: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.228 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.891 109.129 174.492 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
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] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (4z5t.pdb1.gz) 241 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
  • 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
  • Fold representative 4z5t from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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