6LA9 Dna Binding Protein date Nov 12, 2019
title 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assemble Linker Histone H1.0 (High Cryoprotectant)
authors Z.Adhireksan, D.Sharma, P.L.Lee, C.A.Davey
compound source
Molecule: Histone H3.1
Chain: A, E, K, O
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: Hist1h3a, H3fa, Hist1h3b, H3fl, Hist1h3c, H3fc, Hist1 H3fb, Hist1h3e, H3fd, Hist1h3f, H3fi, Hist1h3g, H3fh, Hist1 H3fk, Hist1h3i, H3ff, Hist1h3j, H3fj;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F, L, P
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
Expression_system_taxid: 562

Molecule: Histone H2a Type 1-Be
Chain: C, G, M, Q
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
Expression_system_taxid: 562

Molecule: Histone H2b Type 1-J
Chain: D, H, N, R
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 (349-Mer)
Chain: I
Engineered: Yes

Organism_scientific: Other Sequences
Organism_taxid: 28384
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (349-Mer)
Chain: J
Engineered: Yes

Organism_scientific: Other Sequences
Organism_taxid: 28384
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H1.0
Chain: S, T
Synonym: Histone H1',Histone H1(0)
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H1-0, H1f0, H1fv
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.194 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.780 172.880 216.041 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.70 Å
ligand CA, K enzyme
Primary referenceNear-atomic resolution structures of interdigitated nucleosome fibres., Adhireksan Z, Sharma D, Lee PL, Davey CA, Nat Commun. 2020 Sep 21;11(1):4747. doi: 10.1038/s41467-020-18533-2. PMID:32958761
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (568 Kb) [Save to disk]
  • Biological Unit Coordinates (6la9.pdb1.gz) 546 Kb
  • LPC: Ligand-Protein Contacts for 6LA9
  • CSU: Contacts of Structural Units for 6LA9
  • Structure Factors (1480 Kb)
  • Retrieve 6LA9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6LA9 from S2C, [Save to disk]
  • View 6LA9 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 6LA9
  • 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 6la9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6la9_K] [6la9_I] [6la9_A] [6la9_R] [6la9_F] [6la9_N] [6la9_E] [6la9_L] [6la9_D] [6la9_J] [6la9_C] [6la9_H] [6la9_B] [6la9_S] [6la9_G] [6la9_T] [6la9_P] [6la9_M] [6la9_Q] [6la9_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6LA9
  • Community annotation for 6LA9 at PDBWiki (http://pdbwiki.org)

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