6T90 Transcription date Oct 25, 2019
title Oct4-Sox2-Bound Nucleosome - Shl-6
authors A.K.Michael, G.Kempf, S.Cavadini, R.D.Bunker, N.H.Thoma
compound source
Molecule: Histone H3.1
Chain: A
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-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

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 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

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-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

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-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Histone H3.1
Chain: 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: H3c1, H3fa, Hist1h3a, H3c2, H3fl, Hist1h3b, H3c3, H3f Hist1h3c, H3c4, H3fb, Hist1h3d, H3c6, H3fd, Hist1h3e, H3c7, Hist1h3f, H3c8, H3fh, Hist1h3g, H3c10, H3fk, Hist1h3h, H3c1 Hist1h3i, H3c12, H3fj, Hist1h3j;
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Dna (146-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (146-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Green Fluorescent Protein,Pou Domain, Class 5, Transcription Factor 1;
Chain: K
Synonym: Octamer-Binding Protein 3,Oct-3,Octamer-Binding Pr Oct-4,Octamer-Binding Transcription Factor 3,Otf-3;
Engineered: Yes

Organism_scientific: Aequorea Victoria, Homo Sapiens
Organism_common: Jellyfish, Human
Organism_taxid: 6100, 9606
Gene: Gfp, Pou5f1, Oct3, Oct4, Otf3
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Transcription Factor Sox-2
Chain: L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sox2
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
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 3.05 Å
ligand PTD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


K
  • DNA binding


  • Primary referenceMechanisms of OCT4-SOX2 motif readout on nucleosomes., Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH, Science. 2020 Apr 23. pii: science.abb0074. doi: 10.1126/science.abb0074. PMID:32327602
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (270 Kb) [Save to disk]
  • Biological Unit Coordinates (6t90.pdb1.gz) 259 Kb
  • LPC: Ligand-Protein Contacts for 6T90
  • CSU: Contacts of Structural Units for 6T90
  • Retrieve 6T90 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6T90 from S2C, [Save to disk]
  • View 6T90 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 6T90
  • 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 6t90 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6t90_D] [6t90_K] [6t90_J] [6t90_H] [6t90_I] [6t90_C] [6t90_B] [6t90_F] [6t90_E] [6t90_G] [6t90_A] [6t90_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6T90
  • Community annotation for 6T90 at PDBWiki (http://pdbwiki.org)

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