4QLC Chromatin Binding Protein Dna date Jun 11, 2014
title Crystal Structure Of Chromatosome At 3.5 Angstrom Resolution
authors J.S.Jiang, B.R.Zhou, T.S.Xiao, Y.W.Bai
compound source
Molecule: Dna (167-Mer)
Chain: I
Fragment: 167bp Widom 601 Dna
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Dna
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (167-Mer)
Chain: J
Fragment: 167bp Widom 601 Dna
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Dna
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H3
Chain: A, E
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Strain: 7227
Gene: Cg31613, Cg33803, Cg33806, Cg33809, Cg33812, Cg33815, Cg33821, Cg33824, Cg33827, Cg33830, Cg33833, Cg33836, Cg338 Cg33842, Cg33845, Cg33848, Cg33851, Cg33854, Cg33857, Cg338
Cg33863, Cg33866, H3_drome, His3, His3: Cg31613, His3:Cg3380
His3: Cg33806, His3:Cg33809, His3:Cg33812, His3:Cg33815,
His3: Cg33818, His3:Cg33821, His3:Cg33824, His3:Cg33827,
His3: Cg33830, His3:Cg33833, His3:Cg33836, His3:Cg33839,
His3: Cg33842, His3:Cg33845, His3:Cg33848, His3:Cg33851,
His3: Cg33854, His3:Cg33857, His3:Cg33860, His3:Cg33863,
His3: Cg33866
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: 562

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

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Strain: 7227
Gene: Cg31611, Cg3379, Cg33869, Cg33871, Cg33873, Cg33875, Cg33879, Cg33881, Cg33883, Cg33885, Cg33887, Cg33889, Cg338 Cg33893, Cg33895, Cg33897, Cg33899, Cg33901, Cg33903, Cg339
Cg33907, Cg33909, H4, H4r, H4_drome, His4, His4: Cg31611,
His4: Cg33869, His4:Cg33871, His4:Cg33873, His4:Cg33875,
His4: Cg33877, His4:Cg33879, His4:Cg33881, His4:Cg33883,
His4: Cg33885, His4:Cg33887, His4:Cg33889, His4:Cg33891,
His4: Cg33893, His4:Cg33895, His4:Cg33897, His4:Cg33899,
His4: Cg33901, His4:Cg33903, His4:Cg33905, His4:Cg33907,
His4: Cg33909, His4r
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: 562

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

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Strain: 7227
Gene: Cg31618, Cg33808, Cg33814, Cg33817, Cg33820, Cg33823, Cg33829, Cg33832, Cg33835, Cg33838, Cg33841, Cg33844, Cg338
Cg33850, Cg33862, Cg33865, H2a, H2a_drome, His2a, His2a: Cg3
His2a: Cg33808, His2a:Cg33814, His2a:Cg33817, His2a:Cg33820,
His2a: Cg33823, His2a:Cg33826, His2a:Cg33829, His2a:Cg33832,
His2a: Cg33835, His2a:Cg33838, His2a:Cg33841, His2a:Cg33844,
His2a: Cg33847, His2a:Cg33850, His2a:Cg33862, His2a:Cg33865
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: 562

Molecule: Histone H2b
Chain: D, H
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Strain: 7227
Gene: Cg17949, Cg33868, Cg33870, Cg33872, Cg33874, Cg33876, Cg33880, Cg33882, Cg33884, Cg33886, Cg33888, Cg33890, Cg338 Cg33894, Cg33896, Cg33898, Cg33900, Cg33902, Cg33904, Cg339
Cg33908, Cg33910, H2b_drome, His2b, His2b: Cg17949, His2b:Cg
His2b: Cg33870, His2b:Cg33872, His2b:Cg33874, His2b:Cg33876,
His2b: Cg33878, His2b:Cg33880, His2b:Cg33882, His2b:Cg33884,
His2b: Cg33886, His2b:Cg33888, His2b:Cg33890, His2b:Cg33892,
His2b: Cg33894, His2b:Cg33896, His2b:Cg33898, His2b:Cg33900,
His2b: Cg33902, His2b:Cg33904, His2b:Cg33906, His2b:Cg33908,
His2b: Cg33910
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: 562

Molecule: H5
Chain: U
Engineered: Yes

Organism_scientific: Gallus Gallus
Organism_taxid: 9031
Strain: 9031
Gene: H5_chick
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: 562
symmetry Space Group: P 65
R_factor 0.218 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
262.870 262.870 91.790 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.50 Å
ligand CIT enzyme
Genes H2A, H2B, H3, H4 (D. melanogaster); H5 (G. gallus)
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


U


Primary referenceStructural Mechanisms of Nucleosome Recognition by Linker Histones., Zhou BR, Jiang J, Feng H, Ghirlando R, Xiao TS, Bai Y, Mol Cell. 2015 Jul 22. pii: S1097-2765(15)00497-9. doi:, 10.1016/j.molcel.2015.06.025. PMID:26212454
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (278 Kb) [Save to disk]
  • Biological Unit Coordinates (4qlc.pdb1.gz) 271 Kb
  • LPC: Ligand-Protein Contacts for 4QLC
  • CSU: Contacts of Structural Units for 4QLC
  • Structure Factors (839 Kb)
  • Retrieve 4QLC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4QLC from S2C, [Save to disk]
  • Re-refined 4qlc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4QLC 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 4QLC
  • 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 4qlc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4qlc_C] [4qlc] [4qlc_E] [4qlc_G] [4qlc_J] [4qlc_U] [4qlc_I] [4qlc_D] [4qlc_F] [4qlc_H] [4qlc_A] [4qlc_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4QLC: [H15] [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 4QLC
  • Community annotation for 4QLC at PDBWiki (http://pdbwiki.org)

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