6E0P Nuclear Protein date Jul 06, 2018
title Cryo-Em Structure Of The Centromeric Nucleosome (Native Alph Satellite Dna) In Complex With A Single Chain Antibody Frag
authors K.N.S.Yadav, B.R.Zhou
compound source
Molecule: Histone H3-Like Centromeric Protein A
Chain: A, E
Synonym: Centromere Autoantigen A,Centromere Protein A,Cenp
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cenpa
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: 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
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
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 (145-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (145-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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 2.60 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] (282 Kb) [Save to disk]
  • Biological Unit Coordinates (6e0p.pdb1.gz) 276 Kb
  • CSU: Contacts of Structural Units for 6E0P
  • Retrieve 6E0P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6E0P from S2C, [Save to disk]
  • View 6E0P 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 6E0P
  • 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 6e0p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6e0p_N] [6e0p_E] [6e0p_G] [6e0p_H] [6e0p_C] [6e0p_B] [6e0p_M] [6e0p_F] [6e0p_A] [6e0p_I] [6e0p_J] [6e0p_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6E0P
  • Community annotation for 6E0P at PDBWiki (http://pdbwiki.org)

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