5OY7 Gene Regulation date Sep 07, 2017
title Structure Of The 4_601_157 Tetranucleosome (P1 Form)
authors B.Ekundayo, T.J.Richmond, T.Schalch
compound source
Molecule: Histone H2b 1.1
Chain: L, P, D, H, T, X, b, f
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: Histone H3
Chain: M, Q, I, A, E, U, Y, c
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h3g, H3l
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: N, R, J, B, F, V, Z, d
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: O, C, G, K, S, W, a, e
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: Dna (619-Mer)
Chain: g
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (619-Mer)
Chain: h
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.219 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.624 161.465 227.915 78.94 83.86 83.74
method X-Ray Diffractionresolution 5.77 Å
ligand CL enzyme
Gene
Ontology
ChainFunctionProcessComponent
N, d, Z, J, B, F, V, R


S, a, K, e, W, G, C, O


T, H, b, D, L, f, X, P


Y, E, c, I, U, Q, M, A


Primary referenceCapturing structural heterogeneity in chromatin fibers., Ekundayo B, Richmond TJ, Schalch T, J Mol Biol. 2017 Sep 9. pii: S0022-2836(17)30424-2. doi:, 10.1016/j.jmb.2017.09.002. PMID:28893533
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (889 Kb) [Save to disk]
  • Biological Unit Coordinates (5oy7.pdb1.gz) 878 Kb
  • LPC: Ligand-Protein Contacts for 5OY7
  • CSU: Contacts of Structural Units for 5OY7
  • Structure Factors (2219 Kb)
  • Retrieve 5OY7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OY7 from S2C, [Save to disk]
  • View 5OY7 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 5OY7
  • 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 5oy7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5oy7_P] [5oy7_J] [5oy7_O] [5oy7_K] [5oy7_H] [5oy7_U] [5oy7_A] [5oy7_D] [5oy7_h] [5oy7_c] [5oy7_G] [5oy7_T] [5oy7_e] [5oy7_L] [5oy7_B] [5oy7_X] [5oy7_Z] [5oy7_I] [5oy7_f] [5oy7_g] [5oy7_Q] [5oy7_R] [5oy7_V] [5oy7_N] [5oy7_Y] [5oy7_M] [5oy7_S] [5oy7_a] [5oy7_b] [5oy7_C] [5oy7_F] [5oy7_d] [5oy7_W] [5oy7_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5OY7
  • Community annotation for 5OY7 at PDBWiki (http://pdbwiki.org)

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