6YOV Transcription date Apr 15, 2020
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
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H4c1, H4a, H4fa, Hist1h4a, H4c2, H4i, H4fi, Hist1h4 H4g, H4fg, Hist1h4c, H4c4, H4b, H4fb, Hist1h4d, H4c5, H4 Hist1h4e, H4c6, H4c, H4fc, Hist1h4f, H4c8, H4h, H4fh, His H4c9, H4m, H4fm, Hist1h4i, H4c11, H4e, H4fe, Hist1h4j, H4 H4d, H4fd, Hist1h4k, H4c13, H4k, H4fk, Hist1h4l, H4c14, H H4f2, H4fn, Hist2h4, Hist2h4a, H4c15, H4o, H4fo, Hist2h4b, 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: Histone H4
Chain: 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: Dna (142-Mer)
Chain: I, 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 3.42 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] (258 Kb) [Save to disk]
  • Biological Unit Coordinates (6yov.pdb1.gz) 246 Kb
  • LPC: Ligand-Protein Contacts for 6YOV
  • CSU: Contacts of Structural Units for 6YOV
  • Retrieve 6YOV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YOV from S2C, [Save to disk]
  • View 6YOV 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 6YOV
  • 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 6yov from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6yov_I] [6yov_L] [6yov_G] [6yov_E] [6yov_C] [6yov_H] [6yov_D] [6yov_F] [6yov_J] [6yov_B] [6yov_A] [6yov_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6YOV
  • Community annotation for 6YOV at PDBWiki (http://pdbwiki.org)

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