6R90 Dna Binding Protein date Apr 02, 2019
title Cryo-Em Structure Of Ncp-Thf2(+1)-Uv-Ddb Class A
authors S.Matsumoto, S.Cavadini, R.D.Bunker, N.H.Thoma
compound source
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
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

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 Abasic S Positions 93-94;
Chain: J
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna Damage-Binding Protein 1
Chain: K
Synonym: Ddb P127 Subunit,Dna Damage-Binding Protein A,Ddba Specific Dna-Binding Protein 1,Hbv X-Associated Protein 1,X Damaged Dna-Binding Factor,Uv-Damaged Dna-Binding Protein 1 Xpe-Binding Factor,Xpe-Bf,Xeroderma Pigmentosum Group E-Com Protein,Xpce;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddb1, Xap1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus

Molecule: Dna Damage-Binding Protein 2
Chain: L
Synonym: Ddb P48 Subunit,Ddbb,Damage-Specific Dna-Binding P Uv-Damaged Dna-Binding Protein 2,Uv-Ddb 2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddb2
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
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 4.50 Å
ligand 3DR enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


K


L


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] (708 Kb) [Save to disk]
  • Biological Unit Coordinates (6r90.pdb1.gz) 699 Kb
  • LPC: Ligand-Protein Contacts for 6R90
  • CSU: Contacts of Structural Units for 6R90
  • Retrieve 6R90 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6R90 from S2C, [Save to disk]
    • View 6R90 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 6R90
  • 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 6r90 from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6r90_H] [6r90_E] [6r90_D] [6r90_K] [6r90_J] [6r90_A] [6r90_G] [6r90_C] [6r90_F] [6r90_B] [6r90_I] [6r90_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6R90
  • Community annotation for 6R90 at PDBWiki (http://pdbwiki.org)

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