PDB entry 6j99

View 6j99 on RCSB PDB site
Description: cryo-em structure of human dot1l in complex with an h2b- monoubiquitinated nucleosome
Deposited on 2019-01-22, released 2019-02-27
The last revision was dated 2019-04-10, with a file datestamp of 2019-04-05.
Experiment type: EM
Resolution: 4.1 Å
R-factor: N/A
AEROSPACI score: 0.07 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: histone h3
    Species: Xenopus laevis [TaxId:8355]
    Gene: XELAEV_18002543mg
    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, LOC494591, XELAEV_18003602mg
    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
      • engineered mutation (29)
      • engineered mutation (117)
  • Chain 'E':
    Compound: histone h3
    Species: Xenopus laevis [TaxId:8355]
    Gene: XELAEV_18002543mg
    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, LOC494591, XELAEV_18003602mg
    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 (Start-122)
      • engineered mutation (29)
      • engineered mutation (117)
  • Chain 'I':
    Compound: DNA (144-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: DNA (145-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'K':
    Compound: Histone-lysine N-methyltransferase, H3 lysine-79 specific
    Species: Homo sapiens [TaxId:9606]
    Gene: DOT1L, KIAA1814, KMT4
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62979 (0-75)
      • engineered mutation (75)
  • Heterogens: SAH

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:
    >6j99A (A:)
martkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqssavmalqeaseaylvalfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6j99A (A:)
phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqease
aylvalfedtnlcaihakrvtimpkdiqlarrirger

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6j99B (B:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6j99B (B:)
krhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteh
akrktvtamdvvyalkrqgrtlygfg

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6j99C (C:)
msgrgkqggktrakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleylt
aeilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkk
tessksaksk

    Sequence, based on observed residues (ATOM records):
    >6j99C (C:)
rakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaa
rdnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6j99D (D:)
maksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskamsim
nsfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtcyt
sak

    Sequence, based on observed residues (ATOM records):
    >6j99D (D:)
rktrkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrsti
tsreiqtavrlllpgelakhavsegtkavtcyts

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6j99E (E:)
martkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqssavmalqeaseaylvalfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6j99E (E:)
phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqease
aylvalfedtnlcaihakrvtimpkdiqlarrirger

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6j99F (F:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6j99F (F:)
vlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrkt
vtamdvvyalkrqgrtlygfg

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6j99G (G:)
msgrgkqggktrakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleylt
aeilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkk
tessksaksk

    Sequence, based on observed residues (ATOM records):
    >6j99G (G:)
kaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaard
nkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllp

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6j99H (H:)
maksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskamsim
nsfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtcyt
sak

    Sequence, based on observed residues (ATOM records):
    >6j99H (H:)
ktrkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstit
sreiqtavrlllpgelakhavsegtkavtcytsak

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6j99K (K:)
mgeklelrlkspvgaepavypwplpvydkhhdaaheiietirwvceeipdlklamenyvl
idydtksfesmqrlcdkynraidsihqlwkgttqpmklntrpstgllrhilqqvynhsvt
dpeklnnyepfspevygetsfdlvaqmideikmtdddlfvdlgsgvgqvvlqvaaatnck
hhygvekadipakyaetmdrefrkwmkwygkkhaeytlergdflseewreriantsvifv
nnfafgpevdhqlkerfanmkeggrivsskpfaplnfrinsrnlsdigtimrvvelsplk
gsvswtgkpvsyylhtidrtilenyfsslknpklreeqeaarrrqqresksnaatptkgp
egkvagpadapmdsgaeeekagaatvkkpspskarkkklnkkgrkmagrkrgrpkk

    Sequence, based on observed residues (ATOM records):
    >6j99K (K:)
rlkspvgaepavypwplpvydkhhdaaheiietirwvceeipdlklamenyvlidydtks
fesmqrlcdkynraidsihqlwkgttqpmklntrpstgllrhilqqvynhsvtdpeklnn
yepfspevygetsfdlvaqmideikmtdddlfvdlgsgvgqvvlqvaaatnckhhygvek
adipakyaetmdrefrkwmkwygkkhaeytlergdflseewreriantsvifvnnfafgp
evdhqlkerfanmkeggrivsskpfaplnfrinsrnlsdigtimrvvelsplkgsvswtg
kpvsyylhtidrtilenyfsslkn

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records:
    >6j99L (L:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgc