3UTB Structural Protein Dna date Nov 25, 2011
title Crystal Structure Of Nucleosome Core Particle Assembled With Alpha-Satellite Sequence (Ncp146b)
authors E.Y.D.Chua, D.Vasudevan, G.E.Davey, B.Wu, C.A.Davey
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
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3d

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
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

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
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

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
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

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

Synthetic: Yes
Other_details: Synthetic Construct
symmetry Space Group: P 21 21 21
R_factor 0.232 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.460 109.280 175.920 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand MN, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceThe mechanics behind DNA sequence-dependent properties of the nucleosome., Chua EY, Vasudevan D, Davey GE, Wu B, Davey CA, Nucleic Acids Res. 2012 Mar 26. PMID:22453276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (255 Kb) [Save to disk]
  • Biological Unit Coordinates (3utb.pdb1.gz) 248 Kb
  • LPC: Ligand-Protein Contacts for 3UTB
  • CSU: Contacts of Structural Units for 3UTB
  • Structure Factors (5098 Kb)
  • Retrieve 3UTB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UTB from S2C, [Save to disk]
  • Re-refined 3utb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UTB 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 3UTB
  • 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
  • 3D motif for 3UTB, from MSDmotif at EBI
  • Fold representative 3utb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3utb_I] [3utb_H] [3utb_A] [3utb_G] [3utb_F] [3utb] [3utb_E] [3utb_D] [3utb_C] [3utb_B] [3utb_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3UTB: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3UTB
  • Community annotation for 3UTB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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