6R93 Dna date Apr 02, 2019
title Cryo-Em Structure Of Ncp-6-4pp
authors S.Matsumoto, S.Cavadini, R.D.Bunker, N.H.Thoma
compound source
Molecule: Human Alpha-Satellite Dna (145-Mer)
Chain: I
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Human Alpha-Satellite Dna (145-Mer) With A 6-4pp Positions 95-96;
Chain: J
Engineered: Yes
Other_details: 145 Bp Human Alpha-Satellite With A 6-4 Pyri Pyrimidone (6-4pp) At Base Positions 95-96.;

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

Molecule: Histone H3.1
Chain: A, E
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 Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid

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
Expression_system_cell_line: Jm109(De3)
Expression_system_vector_type: Plasmid

Molecule: Histone H2a Type 1-Be
Chain: C, G
Synonym: Histone H2a.2,Histone H2aa,Histone H2am
Engineered: Yes
Other_details: Gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavl Agnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkkteshh

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
Expression_system_vector_type: Plasmid

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 Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
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 4.00 Å
ligand T64 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceDNA damage detection in nucleosomes involves DNA register shifting., Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH, Nature. 2019 May 29. pii: 10.1038/s41586-019-1259-3. doi:, 10.1038/s41586-019-1259-3. PMID:31142837
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (403 Kb) [Save to disk]
  • Biological Unit Coordinates (6r93.pdb1.gz) 396 Kb
  • LPC: Ligand-Protein Contacts for 6R93
  • CSU: Contacts of Structural Units for 6R93
  • Retrieve 6R93 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6R93 from S2C, [Save to disk]
  • View 6R93 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 6R93
  • 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 6r93 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6r93_D] [6r93_E] [6r93_F] [6r93_H] [6r93_B] [6r93_J] [6r93_C] [6r93_I] [6r93_A] [6r93_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6R93
  • Community annotation for 6R93 at PDBWiki (http://pdbwiki.org)

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