2025-09-17 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY database_2 em_admin _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DERIVED_CALCULATIONS em_admin pdbx_validate_close_contact struct_conn struct_conn_type _em_admin.last_update PDBj PDBj 2019-01-22 2019-02-27 2019-02-27 2025-09-17 Ministry of Science and Technology (China) 2016YFA0501803 China National Natural Science Foundation of China 31570766 China National Natural Science Foundation of China U1632130 China Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Yao T Huang J epigenetics, nucleosome, DOT1L, histone modification, TRANSCRIPTION Yao T Jing W Hu Z Tan M Cao M Wang Q Li Y Yuan G Lei M Huang J Structural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome. Cell Res. CN 29 330 333 2019 30770869 doi:10.1038/s41422-019-0146-7 1748-7838 6j99 FULLOVERLAP EMDB EMD-9783 associated EM volume
Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome
 Human DOT1L in complex with an H2B-monoubiquitinated nucleosome Human DOT1L in complex with an H2B-monoubiquitinated nucleosome 0 1 2 3 4 5 6 7 8 African clawed frog 0.25 Human DOT1L in complex with an H2B-monoubiquitinated nucleosome 2 1 2 3 4 Human Human DOT1L in complex with an H2B-monoubiquitinated nucleosome 3 7 8 Histone H3 Xenopus laevis 0.015435125999999999 2 Escherichia coli LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA A0A310TTQ1 Histone H4 Xenopus laevis 0.011394426 2 Escherichia coli LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A Xenopus laevis 0.014109436 2 Escherichia coli LEVO MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII PRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK Q6AZJ8 Histone H2B 1.1 Xenopus laevis 0.013629911 2 Escherichia coli LEVO MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAH YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTSAK P02281 DNA (144-MER) synthetic construct 0.045138769999999995 1 (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT) DNA DNA (145-MER) synthetic construct 0.045610042999999996 1 (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DG)(DA)(DT) DNA Ubiquitin Homo sapiens 0.008622922 1 Escherichia coli LEVO MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC P62979 Histone-lysine N-methyltransferase, H3 lysine-79 specific Homo sapiens 0.047506156
S-ADENOSYL-L-HOMOCYSTEINE
1 Escherichia coli LEVO MGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNR AIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFV DLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFV NNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRT ILENYFSSLKNPKLREEQEAARRRQQRESKSNAATPTKGPEGKVAGPADAPMDSGAEEEKAGAATVKKPSPSKARKKKLN KKGRKMAGRKRGRPKK Q8TEK3 2.1.1.43 S-ADENOSYL-L-HOMOCYSTEINE 0.000384411 1 SAH singleParticle particle 1 7.5 ETHANE FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) COUNTING 0.98 1 PHASE FLIPPING ONLY
Startup model is from an initial model generated from a subset of the entire dataset
 4.1 FSC 0.143 CUT-OFF 151545 NOT APPLICABLE NOT APPLICABLE emd_9783.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 260.0 260.0 260.0 90.0 90.0 90.0 X Y Z -0.14869481 0.25374833 -0.00034746548 0.009964193 1.3 1.3 1.3 0.028 AUTHOR The main map for the overall structure of human DOT1L-ubNCP complex emd_9783_msk_1.map emd_9783_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 260.0 260.0 260.0 90.0 90.0 90.0 X Y Z -0.10554267 0.16932827 -0.0002533957 0.0088667935 1.3 1.3 1.3 AUTHOR An additional EM map that provides good density for the N-terminal region of DOT1L emd_9783_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 260.0 260.0 260.0 90.0 90.0 90.0 X Y Z -0.15579382 0.29390806 -0.00028153462 0.01179784 1.3 1.3 1.3 AUTHOR An additional EM map that provides good density for the DOT1L-ubiquitin interface