6V2K Nuclear Protein Dna date Nov 24, 2019
title The Nucleosome Structure After H2a-H2b Exchange
authors Y.Arimura, R.Hirano, H.Kurumizaka
compound source
Molecule: Histone 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;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3c1, H3fa, Hist1h3a, H3c2, H3fl, Hist1h3b, H3c3, H3f Hist1h3c, H3c4, H3fb, Hist1h3d, H3c6, H3fd, Hist1h3e, H3c7, Hist1h3f, H3c8, H3fh, Hist1h3g, H3c10, H3fk, Hist1h3h, H3c1 Hist1h3i, H3c12, H3fj, Hist1h3j;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H4c1, H4a, H4fa, Hist1h4a, H4c2, H4i, H4fi, Hist1h4 H4g, H4fg, Hist1h4c, H4c4, H4b, H4fb, Hist1h4d, H4c5, H4 Hist1h4e, H4c6, H4c, H4fc, Hist1h4f, H4c8, H4h, H4fh, His H4c9, H4m, H4fm, Hist1h4i, H4c11, H4e, H4fe, Hist1h4j, H4 H4d, H4fd, Hist1h4k, H4c13, H4k, H4fk, Hist1h4l, H4c14, H H4f2, H4fn, Hist2h4, Hist2h4a, H4c15, H4o, H4fo, Hist2h4b, Hist4h4;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a
Chain: C, G
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ab, Hist1h2ae, Hcg_1640984, Hcg_1787383
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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
Expression_system_taxid: 562

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.197 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.561 107.711 168.158 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand CL, MN enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (248 Kb) [Save to disk]
  • Biological Unit Coordinates (6v2k.pdb1.gz) 237 Kb
  • LPC: Ligand-Protein Contacts for 6V2K
  • CSU: Contacts of Structural Units for 6V2K
  • Structure Factors (1441 Kb)
  • Retrieve 6V2K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6V2K from S2C, [Save to disk]
  • View 6V2K 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 6V2K
  • 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 6v2k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6v2k_J] [6v2k_E] [6v2k_C] [6v2k_I] [6v2k_A] [6v2k_H] [6v2k_G] [6v2k_B] [6v2k_D] [6v2k_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6V2K
  • Community annotation for 6V2K at PDBWiki (http://pdbwiki.org)

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