6DZT Nuclear Protein date Jul 05, 2018
title Cryo-Em Structure Of Nucleosome In Complex With A Single Cha Antibody Fragment
authors K.N.S.Yadav, B.R.Zhou
compound source
Molecule: Histone H3
Chain: A, E
Engineered: Yes
 Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: His3, His3:Cg31613, Cg31613, His3:Cg33803, Cg33803,
His3: Cg33806, Cg33806, His3:Cg33809, Cg33809, His3:Cg33812,
His3: Cg33815, Cg33815, His3:Cg33818, Cg33818, His3:Cg33821,
His3: Cg33824, Cg33824, His3:Cg33827, Cg33827, His3:Cg33830,
His3: Cg33833, Cg33833, His3:Cg33836, Cg33836, His3:Cg33839,
His3: Cg33842, Cg33842, His3:Cg33845, Cg33845, His3:Cg33848,
His3: Cg33851, Cg33851, His3:Cg33854, Cg33854, His3:Cg33857,
His3: Cg33860, Cg33860, His3:Cg33863, Cg33863, His3:Cg33866,
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
Engineered: Yes
Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: His4, H4, His4r, H4r, Cg3379, His4:Cg31611, Cg31611,
His4: Cg33869, Cg33869, His4:Cg33871, Cg33871, His4:Cg33873,
His4: Cg33875, Cg33875, His4:Cg33877, Cg33877, His4:Cg33879,
His4: Cg33881, Cg33881, His4:Cg33883, Cg33883, His4:Cg33885,
His4: Cg33887, Cg33887, His4:Cg33889, Cg33889, His4:Cg33891,
His4: Cg33893, Cg33893, His4:Cg33895, Cg33895, His4:Cg33897,
His4: Cg33899, Cg33899, His4:Cg33901, Cg33901, His4:Cg33903,
His4: Cg33905, Cg33905, His4:Cg33907, Cg33907, His4:Cg33909,
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a
Chain: C, G
Engineered: Yes
Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: His2a, H2a, His2a:Cg31618, Cg31618, His2a:Cg33808, Cg
His2a: Cg33814, Cg33814, His2a:Cg33817, Cg33817, His2a:Cg338
Cg33820, His2a: Cg33823, Cg33823, His2a:Cg33826, Cg33826,
His2a: Cg33829, Cg33829, His2a:Cg33832, Cg33832, His2a:Cg338
Cg33835, His2a: Cg33838, Cg33838, His2a:Cg33841, Cg33841,
His2a: Cg33844, Cg33844, His2a:Cg33847, Cg33847, His2a:Cg338
Cg33850, His2a: Cg33862, Cg33862, His2a:Cg33865, Cg33865
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b
Chain: D, H
Engineered: Yes
Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: His2b, His2b:Cg17949, Cg17949, His2b:Cg33868, Cg33868
His2b: Cg33870, Cg33870, His2b:Cg33872, Cg33872, His2b:Cg338
Cg33874, His2b: Cg33876, Cg33876, His2b:Cg33878, Cg33878,
His2b: Cg33880, Cg33880, His2b:Cg33882, Cg33882, His2b:Cg338
Cg33884, His2b: Cg33886, Cg33886, His2b:Cg33888, Cg33888,
His2b: Cg33890, Cg33890, His2b:Cg33892, Cg33892, His2b:Cg338
Cg33894, His2b: Cg33896, Cg33896, His2b:Cg33898, Cg33898,
His2b: Cg33900, Cg33900, His2b:Cg33902, Cg33902, His2b:Cg339
Cg33904, His2b: Cg33906, Cg33906, His2b:Cg33908, Cg33908,
His2b: Cg33910, Cg33910
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (147-Mer)
Chain: I
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Dna (147-Mer)
Chain: J
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Scfv
Chain: M, N
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 2.99 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceAtomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment., Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P, Nat Commun. 2019 May 24;10(1):2301. doi: 10.1038/s41467-019-10247-4. PMID:31127102
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk]
  • Biological Unit Coordinates (6dzt.pdb1.gz) 278 Kb
  • CSU: Contacts of Structural Units for 6DZT
  • Retrieve 6DZT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6DZT from S2C, [Save to disk]
    • View 6DZT 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 6DZT
  • 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: [6dzt_G] [6dzt_H] [6dzt_E] [6dzt_F] [6dzt_M] [6dzt_I] [6dzt_A] [6dzt_D] [6dzt_B] [6dzt_J] [6dzt_N] [6dzt_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6DZT
  • Community annotation for 6DZT at PDBWiki (http://pdbwiki.org)

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