PDB entry 6jma

View 6jma on RCSB PDB site
Description: cryo-em structure of dot1l bound to h2b ubiquitinated nucleosome
Deposited on 2019-03-07, released 2019-05-15
The last revision was dated 2019-11-06, with a file datestamp of 2019-11-01.
Experiment type: EM
Resolution: 6.8 Å
R-factor: N/A
AEROSPACI score: -0.04 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.2
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: histone h2a
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h2aj
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P02281 (1-93)
      • expression tag (0)
  • Chain 'E':
    Compound: Histone H3.2
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: histone h2a
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h2aj
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P02281 (1-93)
      • expression tag (0)
  • Chain 'I':
    Compound: DNA I&j
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: DNA I&j
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'X':
    Compound: Histone-lysine N-methyltransferase, H3 lysine-79 specific
    Species: Homo sapiens [TaxId:9606]
    Gene: dot1l
    Database cross-references and differences (RAF-indexed):
  • Chain 'Y':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed):
  • Heterogens: SAM

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; same for both SEQRES and ATOM records:
    >6jmaA (A:)
    phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqease
    aylvglfedtnlcaihakrvtimpkdiqlarrirgera
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6jmaB (B:)
    krhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteh
    akrktvtamdvvyalkrqgrtlygfgg
    

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

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6jmaC (C:)
    aktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardn
    kktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkktessksaksk
    

    Sequence, based on observed residues (ATOM records):
    >6jmaC (C:)
    aktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardn
    kktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkkt
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >6jmaD (D:)
    trkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstits
    reiqtavrlllpgelakhavsegtkavtkytsak
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >6jmaE (E:)
    phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqease
    aylvglfedtnlcaihakrvtimpkdiqlarrirgera
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >6jmaF (F:)
    krhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteh
    akrktvtamdvvyalkrqgrtlygfgg
    

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6jmaG (G:)
    aktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardn
    kktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkktessksaksk
    

    Sequence, based on observed residues (ATOM records):
    >6jmaG (G:)
    aktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardn
    kktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkk
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records:
    >6jmaH (H:)
    trkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstits
    reiqtavrlllpgelakhavsegtkavtkytsak
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records:
    >6jmaX (X:)
    lelrlkspvgaepavypwplpvydkhhdaaheiietirwvceeipdlklamenyvlidyd
    tksfesmqrlcdkynraidsihqlwkgttqpmklntrpstgllrhilqqvynhsvtdpek
    lnnyepfspevygetsfdlvaqmideikmtdddlfvdlgsgvgqvvlqvaaatnckhhyg
    vekadipakyaetmdrefrkwmkwygkkhaeytlergdflseewreriantsvifvnnfa
    fgpevdhqlkerfanmkeggrivsskpfaplnfrinsrnlsdigtimrvvelsplkgsvs
    wtgkpvsyylhtidrtilenyfsslknp
    

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records:
    >6jmaY (Y:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrgg