3WA9 Structural Protein Dna date Apr 30, 2013
title The Nucleosome Containing Human H2a.Z.1
authors N.Horikoshi, K.Sato, K.Shimada, Y.Arimura, A.Osakabe, H.Tachiwana W.Iwasaki, W.Kagawa, M.Harata, H.Kimura, H.Kurumizaka
compound source
Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a, Histone H3b, Histone H3c, Histone Histone H3f, Histone H3h, Histone H3i, Histone H3j, His Histone H3l;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H2a.Z
Chain: C, G
Synonym: H2az
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2a.Z.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

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: H2b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

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

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.222 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.903 109.390 181.764 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.07 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceStructural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2., Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, Kurumizaka H, Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2431-9. doi:, 10.1107/S090744491302252X. Epub 2013 Nov 19. PMID:24311584
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (246 Kb) [Save to disk]
  • Biological Unit Coordinates (3wa9.pdb1.gz) 239 Kb
  • CSU: Contacts of Structural Units for 3WA9
  • Structure Factors (629 Kb)
  • Retrieve 3WA9 in mmCIF format [Save to disk]
  • Re-refined 3wa9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WA9 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 3WA9
  • 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 3WA9, from MSDmotif at EBI
  • Fold representative 3wa9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wa9] [3wa9_B] [3wa9_H] [3wa9_A] [3wa9_F] [3wa9_C] [3wa9_I] [3wa9_G] [3wa9_J] [3wa9_D] [3wa9_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3WA9: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3WA9
  • Community annotation for 3WA9 at PDBWiki (http://pdbwiki.org)

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