5ZBX Dna Binding Protein Dna date Feb 13, 2018
title The Crystal Structure Of The Nucleosome Containing Histone H Catd(V76q, K77d)
authors Y.Arimura, H.Takagi, H.Kurumizaka
compound source
Molecule: Histone H3.1,Histone H3-Like Centromeric Protein H3.1;
Chain: A, E
Synonym: Histone H3a,Histone H3b,Histone H3c,Histone H3 H3f,Histone H3h,Histone H3i,Histone H3j,Histone H3k,Hi H3l,Centromere Autoantigen A,Centromere Protein A,Cenp-A;
Engineered: Yes
Mutation: Yes
Other_details: Chimera Protein H3catd, In Which Amino Acid 76-113 Of Human Histone H3.1 Were Replaced By The Correspon Acid Residues 75-114 Of Human Cenp-A.;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h3a, H3fa, Hist1h3b, H3fl, Hist1h3c, H3fc, Hist1 H3fb, Hist1h3e, H3fd, Hist1h3f, H3fi, Hist1h3g, H3fh, Hist1 H3fk, Hist1h3i, H3ff, Hist1h3j, H3fj, Cenpa;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ph3.1 Catd

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a, H4a, H4fa, Hist1h4b, H4i, H4fi, Hist1h4c, H4fg, Hist1h4d, H4b, H4fb, Hist1h4e, H4j, H4fj, Hist1h4f, H4fc, Hist1h4h, H4h, H4fh, Hist1h4i, H4m, H4fm, Hist1h4j, H4fe, Hist1h4k, H4d, H4fd, Hist1h4l, H4k, H4fk, Hist2h4a, H4f2, H4fn, Hist2h4, Hist2h4b, H4o, H4fo, Hist4h4;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
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, H2afm, Hist1h2ae, H2afa
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
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)

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

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli Dh5alpha
Expression_system_taxid: 668369
Expression_system_strain: Dh5alpha
Expression_system_vector_type: Plasmid
symmetry Space Group: P 21 21 21
R_factor 0.213 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.543 109.003 170.136 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.58 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceThe CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism., Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H, Fukagawa T, Kurumizaka H, Nat Commun. 2019 Feb 4;10(1):576. doi: 10.1038/s41467-019-08314-x. PMID:30718488
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk]
  • Biological Unit Coordinates (5zbx.pdb1.gz) 241 Kb
  • LPC: Ligand-Protein Contacts for 5ZBX
  • CSU: Contacts of Structural Units for 5ZBX
  • Structure Factors (1507 Kb)
  • Retrieve 5ZBX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ZBX from S2C, [Save to disk]
  • View 5ZBX 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 5ZBX
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5zbx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5zbx_H] [5zbx_C] [5zbx_E] [5zbx_I] [5zbx_F] [5zbx_B] [5zbx_A] [5zbx_G] [5zbx_J] [5zbx_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5ZBX
  • Community annotation for 5ZBX at PDBWiki (http://pdbwiki.org)

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