6HKT Dna Binding Protein date Sep 08, 2018
title Structure Of An H1-Bound 6-Nucleosome Array
authors I.Garcia-Saez, S.Dimitrov, C.Petosa
compound source
Molecule: Histone H3.1
Chain: A, E, a, e, K, O, k, o, U, Y, u, y
Synonym: Histone H3a,Histone H3b,Histone H3c,Histone H3 H3f,Histone H3h,Histone H3i,Histone H3j,Histone H3k,Hi H3l;
Engineered: Yes
Other_details: The 3 N-Terminal Residues (Gsh) Come From Th Expression Tag;
 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;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Histone H4
Chain: B, F, b, f, L, P, l, p, V, Z, v, z
Engineered: Yes
Other_details: The 3 N-Terminal Residues (Gsh) Come From Th Expression Tag;
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

Molecule: Histone H2a Type 1-Be
Chain: C, G, c, g, M, Q, m, q, W, 0, w, 2
Synonym: Histone H2a.2,Histone H2aa,Histone H2am
Engineered: Yes
Other_details: The 3 N-Terminal Residues (Gsh) Come From Th Expression Tag;
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

Molecule: Histone H2b Type 1-J
Chain: D, H, d, h, N, R, n, r, X, 1, x, 3
Synonym: Histone H2b.1,Histone H2b.R,H2br
Engineered: Yes
Other_details: The 3 N-Terminal Residues (Gsh) Come From Th Expression Tag;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bj, H2bfr
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna (1122-Mer)
Chain: I
Engineered: Yes
Other_details: Six Tandem 187-Bp Repeats Containing Widom 6 Sequence;
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (1122-Mer)
Chain: J
Engineered: Yes
Other_details: Six Tandem 187-Bp Repeats Containing Widom 6 Sequence
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 2 21 21
R_factor 0.254 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.078 238.761 674.368 90.00 90.00 90.00
method X-Ray Diffractionresolution 9.70 Å
Gene
Ontology
ChainFunctionProcessComponent
2, g, W, c, q, G, w, Q, M, C, 0, m


N, d, 1, H, D, r, x, h, n, 3, X, R


Z, v, B, b, z, F, V, L, f, P, l, p


a, K, Y, E, y, u, k, e, U, A, O, o


Primary referenceStructure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation., Garcia-Saez I, Menoni H, Boopathi R, Shukla MS, Soueidan L, Noirclerc-Savoye M, Le Roy A, Skoufias DA, Bednar J, Hamiche A, Angelov D, Petosa C, Dimitrov S, Mol Cell. 2018 Oct 22. pii: S1097-2765(18)30798-6. doi:, 10.1016/j.molcel.2018.09.027. PMID:30392928
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1441 Kb) [Save to disk]
  • Biological Unit Coordinates (6hkt.pdb1.gz) 1429 Kb
  • CSU: Contacts of Structural Units for 6HKT
  • Structure Factors (613 Kb)
  • Retrieve 6HKT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6HKT from S2C, [Save to disk]
    • View 6HKT 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 6HKT
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6hkt_a] [6hkt_v] [6hkt_p] [6hkt_D] [6hkt_h] [6hkt_Z] [6hkt_2] [6hkt_3] [6hkt_L] [6hkt_u] [6hkt_c] [6hkt_B] [6hkt_Q] [6hkt_M] [6hkt_g] [6hkt_N] [6hkt_y] [6hkt_b] [6hkt_d] [6hkt_P] [6hkt_U] [6hkt_C] [6hkt_K] [6hkt_z] [6hkt_q] [6hkt_J] [6hkt_Y] [6hkt_X] [6hkt_o] [6hkt_f] [6hkt_A] [6hkt_l] [6hkt_F] [6hkt_H] [6hkt_w] [6hkt_e] [6hkt_n] [6hkt_R] [6hkt_1] [6hkt_I] [6hkt_G] [6hkt_V] [6hkt_E] [6hkt_m] [6hkt_r] [6hkt_k] [6hkt_W] [6hkt_0] [6hkt_O] [6hkt_x]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6HKT
  • Community annotation for 6HKT at PDBWiki (http://pdbwiki.org)

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