4YS3 Structural Protein Dna date Mar 16, 2015
title Nucleosome Disassembly By Rsc And Swisnf Is Enhanced By H3 Acetylation Near The Nucleosome Dyad Axis
authors M.L.Dechassa, K.Luger, N.Chatterjee, J.A.North, M.Manohar, R.Pras J.J.Ottessen, M.G.Poirier, B.Bartholomew
compound source
Molecule: Histone H3.2
Chain: A, E
Fragment: Residues 39-136
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
Fragment: Residues 25-103
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
Fragment: Residues 15-121
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
Fragment: Residues 34-126
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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (147-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.226 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.510 109.620 181.230 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand ALY enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceHistone acetylation near the nucleosome dyad axis enhances nucleosome disassembly by RSC and SWI/SNF., Chatterjee N, North JA, Dechassa ML, Manohar M, Prasad R, Luger K, Ottesen JJ, Poirier MG, Bartholomew B, Mol Cell Biol. 2015 Sep 28. pii: MCB.00441-15. PMID:26416878
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (248 Kb) [Save to disk]
  • Biological Unit Coordinates (4ys3.pdb1.gz) 243 Kb
  • LPC: Ligand-Protein Contacts for 4YS3
  • CSU: Contacts of Structural Units for 4YS3
  • Structure Factors (1074 Kb)
  • Retrieve 4YS3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YS3 from S2C, [Save to disk]
  • Re-refined 4ys3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YS3 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 4YS3
  • 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 4ys3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ys3_I] [4ys3_G] [4ys3_E] [4ys3_J] [4ys3_A] [4ys3_H] [4ys3_D] [4ys3] [4ys3_B] [4ys3_C] [4ys3_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YS3: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 4YS3
  • Community annotation for 4YS3 at PDBWiki (http://pdbwiki.org)

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