PDB entry 6nog

View 6nog on RCSB PDB site
Description: poised-state dot1l bound to the h2b-ubiquitinated nucleosome
Deposited on 2019-01-16, released 2019-02-20
The last revision was dated 2020-01-08, with a file datestamp of 2020-01-03.
Experiment type: EM
Resolution: 3.9 Å
R-factor: N/A
AEROSPACI score: 0.06 (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):
    • Uniprot P84233
      • engineered mutation (101)
  • Chain 'B':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Histone H2A type 1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06897
      • engineered mutation (98)
  • Chain 'D':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P02281
      • engineered mutation (28)
      • engineered mutation (116)
  • Chain 'E':
    Compound: Histone H3.2
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84233
      • engineered mutation (101)
  • Chain 'F':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Histone H2A type 1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06897
      • engineered mutation (98)
  • Chain 'H':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P02281 (Start-121)
      • engineered mutation (28)
      • engineered mutation (116)
  • Chain 'I':
    Compound: 601 DNA Strand 1
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: 601 DNA strand 2
    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: UBB
    Database cross-references and differences (RAF-indexed):

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:
    >6nogA (A:)
artkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkstel
lirklpfqrlvreiaqdfktdlrfqssavmalqeaseaylvalfedtnlcaihakrvtim
pkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6nogA (A:)
phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqease
aylvalfedtnlcaihakrvtimpkdiqlarrirge

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6nogB (B:)
sgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkv
flenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6nogB (B:)
niqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktvtam
dvvyalkrqgrtlygfgg

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6nogC (C:)
sgrgkqggktrakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleylta
eilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkkt
essksaksk

    Sequence, based on observed residues (ATOM records):
    >6nogC (C:)
aktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardn
kktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllp

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6nogD (D:)
aksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskamsimn
sfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtcyts
ak

    Sequence, based on observed residues (ATOM records):
    >6nogD (D:)
trkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstits
reiqtavrlllpgelakhavsegtkavtcytsa

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6nogE (E:)
artkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkstel
lirklpfqrlvreiaqdfktdlrfqssavmalqeaseaylvalfedtnlcaihakrvtim
pkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6nogE (E:)
phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqease
aylvalfedtnlcaihakrvtimpkdiqlarrirge

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6nogF (F:)
sgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkv
flenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6nogF (F:)
vlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrkt
vtamdvvyalkrqgrtlygfgg

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6nogG (G:)
sgrgkqggktrakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleylta
eilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkkt
essksaksk

    Sequence, based on observed residues (ATOM records):
    >6nogG (G:)
aktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardn
kktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6nogH (H:)
aksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskamsimn
sfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtcyts
ak

    Sequence, based on observed residues (ATOM records):
    >6nogH (H:)
trkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstits
reiqtavrlllpgelakhavsegtkavtcytsak

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

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

    Sequence, based on observed residues (ATOM records):
    >6nogK (K:)
klelrlkspvgaepavypwplpvydkhhdaaheiietirwvceeipdlklamenylidyd
tksfesmqrlcdkynraidsihqlwkgttqpmklntrpstgllrhilqqvynhsvtdget
sfdlvaqmideikmtdddlfvdlgsgvgqvvlqvaaatnckhhygvekadipakyaetmd
refrkwmkwygkkhaeytlergdflseewreriantsvifvnnfafgpevdhqlkerfan
mkeggrivsskpfaplnfrinsrnlsdigtimrvvelsplkvsyylhtidrtilenyfss
lk

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6nogL (L:)
gshmmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtl
sdyniqkestlhlvlrlrgc

    Sequence, based on observed residues (ATOM records):
    >6nogL (L:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlr