3WTP Dna Binding Protein Dna date Apr 14, 2014
title Crystal Structure Of The Heterotypic Nucleosome Containing H A And H3.3
authors Y.Arimura, K.Shirayama, N.Horikoshi, R.Fujita, W.Kagawa, T.Fukaga G.Almouzni, H.Kurumizaka
compound source
Molecule: Histone H3-Like Centromeric Protein A
Chain: A
Synonym: Centromere Autoantigen A, Centromere Protein A, Ce
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cenpa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19

Molecule: Histone H4
Chain: B, F
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3.3, H4a, H4b, H4c, H4d, H4e, H4g, H4h, H4i, H4k, H4m, H4n, H4o, H4f2, H4fa, H4fb, H4fc, H4fd, H4fe, H4fh, H4fi, H4fj, H4fk, H4fm, H4fn, H4fo, Hist1h4a, Hist1h4 Hist1h4c, Hist1h4d, Hist1h4e, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4l, Hist2h4, Hist2h4a, Hist2h4b,
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19

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: H2afa, H2afm, H4, Hist1h2ab, Hist1h2ae
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

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: H2a, H2bfr, Hist1h2bj
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19

Molecule: Histone H3.3
Chain: E
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2b, H3.3a, H3.3b, H3f3, H3f3a, H3f3b, Pp781
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19

Molecule: Dna (146-Mer)
Chain: I, J
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.229 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.117 107.667 168.143 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.67 Å
Gene
Ontology
ChainFunctionProcessComponent
A


C, G


E


F, B


H, D


Primary referenceCrystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3., Arimura Y, Shirayama K, Horikoshi N, Fujita R, Taguchi H, Kagawa W, Fukagawa T, Almouzni G, Kurumizaka H, Sci Rep. 2014 Nov 19;4:7115. doi: 10.1038/srep07115. PMID:25408271
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (241 Kb) [Save to disk]
  • Biological Unit Coordinates (3wtp.pdb1.gz) 234 Kb
  • CSU: Contacts of Structural Units for 3WTP
  • Structure Factors (1077 Kb)
  • Retrieve 3WTP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WTP from S2C, [Save to disk]
  • Re-refined 3wtp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3WTP 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 3WTP
  • 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
  • 3D motif for 3WTP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wtp_J] [3wtp_C] [3wtp_H] [3wtp_B] [3wtp_D] [3wtp_F] [3wtp_E] [3wtp_G] [3wtp] [3wtp_A] [3wtp_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3WTP: [H2A] [H2B] [H3] [H4 ] by SMART
    • Other resources with information on 3WTP
  • Community annotation for 3WTP at PDBWiki (http://pdbwiki.org)

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