5GSE Structural Protein Dna date Aug 16, 2016
title Crystal Structure Of Unusual Nucleosome
authors D.Kato, A.Osakabe, Y.Arimura, S.Y.Park, H.Kurumizaka
compound source
Molecule: Histone H3.1
Chain: A, E, K, O
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h3a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph3.1

Molecule: Histone H4
Chain: B, F, L, P
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph4

Molecule: Histone H2a Type 1-Be
Chain: C, G, M
Synonym: Histone H2a.2,Histone H2aa,Histone H2am
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ab
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph2a

Molecule: Histone H2b Type 1-J
Chain: D, H, N
Synonym: Histone H2b.1,Histone H2b.R,H2br
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bj
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph2b

Molecule: Dna (250-Mer)
Chain: I
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T Easy

Molecule: Dna (250-Mer)
Chain: J
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T Easy
symmetry Space Group: P 1
R_factor 0.197 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.582 101.804 102.427 119.30 106.51 91.36
method X-Ray Diffractionresolution 3.14 Å
ligand 5CM enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, O, K, E


F, P, B, L


M, C, G


N, H, D


Primary referenceCrystal structure of the overlapping dinucleosome composed of hexasome and octasome., Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H, Science. 2017 Apr 14;356(6334):205-208. doi: 10.1126/science.aak9867. PMID:28408607
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (414 Kb) [Save to disk]
  • Biological Unit Coordinates (5gse.pdb1.gz) 405 Kb
  • LPC: Ligand-Protein Contacts for 5GSE
  • CSU: Contacts of Structural Units for 5GSE
  • Structure Factors (1315 Kb)
  • Retrieve 5GSE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GSE from S2C, [Save to disk]
  • Re-refined 5gse structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GSE 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 5GSE
  • 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 5gse from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gse_L] [5gse_C] [5gse_N] [5gse_P] [5gse] [5gse_F] [5gse_D] [5gse_A] [5gse_G] [5gse_O] [5gse_H] [5gse_M] [5gse_E] [5gse_J] [5gse_I] [5gse_K] [5gse_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5GSE
  • Community annotation for 5GSE at PDBWiki (http://pdbwiki.org)

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