PDB entry 6yov

View 6yov on RCSB PDB site
Description: oct4-sox2-bound nucleosome - shl+6
Deposited on 2020-04-15, released 2020-05-06
The last revision was dated 2020-07-08, with a file datestamp of 2020-07-03.
Experiment type: EM
Resolution: 3.42 Å
R-factor: N/A
AEROSPACI score: 0.12 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: DNA (142-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: DNA (142-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'K':
    Compound: Green fluorescent protein,POU domain, class 5, transcription factor 1
    Species: Homo sapiens [TaxId:9606]
    Gene: POU5F1, OCT3, OCT4, OTF3
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: transcription factor sox-2
    Species: Homo sapiens [TaxId:9606]
    Gene: SOX2
    Database cross-references and differences (RAF-indexed):
  • Heterogens: PTD

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6yovA (A:)
gshmartkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqk
stellirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakr
vtimpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6yovA (A:)
hryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeacea
ylvglfedtnlcaihakrvtimpkdiqlarrirge

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6yovB (B:)
gshmsgrgkggkglgkggakrhrvlrdniqgitkpairrlarrggvkrisgliyeetrgv
lkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6yovB (B:)
vlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrkt
vtamdvvyalkrqgrtlygfgg

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6yovC (C:)
gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
pkkteshhkakgk

    Sequence, based on observed residues (ATOM records):
    >6yovC (C:)
gkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelag
naardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllp

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6yovD (D:)
gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
avtkytsa

    Sequence, based on observed residues (ATOM records):
    >6yovD (D:)
srkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstits
reiqtavrlllpgelakhavsegtkavtkytsa

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6yovE (E:)
gshmartkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqk
stellirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakr
vtimpkdiqlarrirge

    Sequence, based on observed residues (ATOM records):
    >6yovE (E:)
hryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeacea
ylvglfedtnlcaihakrvtimpkdiqlarrirge

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6yovF (F:)
gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6yovF (F:)
lrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktv
tamdvvyalkrqgrtlygfg

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6yovG (G:)
gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
pkkteshhkakgk

    Sequence, based on observed residues (ATOM records):
    >6yovG (G:)
gkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelag
naardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllp

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6yovH (H:)
gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
avtkytsa

    Sequence, based on observed residues (ATOM records):
    >6yovH (H:)
rkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstitsr
eiqtavrlllpgelakhavsegtkavtkytsa

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6yovK (K:)
mdwshpqfeksavdenlyfqggmvskgeelftgvvpilveldgdvnghkfsvsgegegda
tygkltlkficttgklpvpwptlvttltygvqcfsrypdhmkqhdffksampegyvqert
iffkddgnyktraevkfegdtlvnrielkgidfkedgnilghkleynynshnvyimadkq
kngikvnfkirhniedgsvqladhyqqntpigdgpvllpdnhylstqsklskdpnekrdh
mvllefvtaagitlgmdelykeaaakeaaakmaghlasdfafspppggggdgpggpepgw
vdprtwlsfqgppggpgigpgvgpgsevwgippcpppyefcggmaycgpqvgvglvpqgg
letsqpegeagvgvesnsdgaspepctvtpgavklekekleqnpeesqdikalqkeleqf
akllkqkritlgytqadvgltlgvlfgkvfsqtticrfealqlsfknmcklrpllqkwve
eadnnenlqeickaetlvqarkrkrtsienrvrgnlenlflqcpkptlqqishiaqqlgl
ekdvvrvwfcnrrqkgkrsssdyaqredfeaagspfsggpvsfplapgphfgtpgygsph
ftalyssvpfpegeafppvsvttlgspmhsn

    Sequence, based on observed residues (ATOM records):
    >6yovK (K:)
alqkeleqfakllkqkritlgytqadvgltlgvlfgkvfsqtticrfealqlsfknmckl
rpllqkwv

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6yovL (L:)
mdwshpqfeksavdenlyfqggmspdrvkrpmnafmvwsrgqrrkmaqenpkmhnseisk
rlgaewkllsetekrpfideakrlralhmkehpdykyrprrktkt

    Sequence, based on observed residues (ATOM records):
    >6yovL (L:)
vkrpmnafmvwsrgqrrkmaqenpkmhnseiskrlgaewkllsetekrpfideakrlral
hmkehpdykyrpr