6ESF Gene Regulation date Oct 20, 2017
title Nucleosome : Class 1
authors S.Bilokapic, M.Halic
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
 Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a
Chain: C, G
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (147-Mer)
Chain: I
Engineered: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630

Molecule: Dna (147-Mer)
Chain: J
Engineered: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.70 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceHistone octamer rearranges to adapt to DNA unwrapping., Bilokapic S, Strauss M, Halic M, Nat Struct Mol Biol. 2018 Jan;25(1):101-108. doi: 10.1038/s41594-017-0005-5. Epub, 2017 Dec 11. PMID:29323273
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (218 Kb) [Save to disk]
  • Biological Unit Coordinates (6esf.pdb1.gz) 213 Kb
  • CSU: Contacts of Structural Units for 6ESF
  • Retrieve 6ESF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6ESF from S2C, [Save to disk]
    • View 6ESF 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 6ESF
  • 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 6esf from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6esf_G] [6esf_B] [6esf_D] [6esf_I] [6esf_A] [6esf_F] [6esf_E] [6esf_J] [6esf_H] [6esf_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6ESF
  • Community annotation for 6ESF at PDBWiki (http://pdbwiki.org)

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