5X7X Structural Protein Dna date Feb 27, 2017
title The Crystal Structure Of The Nucleosome Containing H3.3 At 2 Angstrom Resolution
authors Y.Arimura, H.Taguchi, H.Kurumizaka
compound source
Molecule: Histone H3.3
Chain: A, E
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3f3a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph3.3

Molecule: Histone H4
Chain: B, F
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
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(De)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph2a

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bj, H2bfr
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

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

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5-Alpha
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T(Easy)
symmetry Space Group: P 21 21 21
R_factor 0.227 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.887 107.509 167.415 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.18 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceCrystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8., Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H, Biochemistry. 2017 Apr 10. doi: 10.1021/acs.biochem.6b01098. PMID:28374988
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (257 Kb) [Save to disk]
  • Biological Unit Coordinates (5x7x.pdb1.gz) 249 Kb
  • LPC: Ligand-Protein Contacts for 5X7X
  • CSU: Contacts of Structural Units for 5X7X
  • Structure Factors (2266 Kb)
  • Retrieve 5X7X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5X7X from S2C, [Save to disk]
  • Re-refined 5x7x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5X7X 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 5X7X
  • 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 5x7x from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5x7x_F] [5x7x_D] [5x7x_B] [5x7x_A] [5x7x_J] [5x7x_C] [5x7x_G] [5x7x_I] [5x7x] [5x7x_E] [5x7x_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5X7X
  • Community annotation for 5X7X at PDBWiki (http://pdbwiki.org)

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