2024-12-18 REL PDBe PDBe PDBe 2023-10-27 2024-10-23 2024-10-23 2024-12-18 Wellcome Trust 210493/Z/18/Z United Kingdom Medical Research Council (MRC, United Kingdom) T029471/1 United Kingdom Wapenaar H Wilson MD Chromatin, Nucleosome, methyltransferase, Ubiquitin, DNA BINDING PROTEIN Wapenaar H Clifford G Rolls W Pasquier M Burdett H Zhang Y Deak G Zou J Spanos C Taylor MRD Mills J Watson JA Kumar D Clark R Das A Valsakumar D Bramham J Voigt P Sproul D Wilson MD Embo Rep. UK 25 5743 5779 2024 39528729 doi:10.1038/s44319-024-00306-3 1469-3178 8qzm FULLOVERLAP DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrapped with 195bp of Widom-601 positioning DNA DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrapped with 195bp of Widom-601 positioning DNA 0 1 2 3 4 5 6 7 Homo sapiens 0.147 H2AKc119ub Nucleosome wrapped with 195 bp Widom601 DNA 1 1 2 3 4 5 6 Homo sapiens DNMT3A1-DNMT3L complex 1 7 Homo sapiens Ubiquitin 1 Homo sapiens Histone H3 (Fragment) Homo sapiens 0.015257838 2 Escherichia coli LEVO ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT DLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA A0A7K7T3V7 Histone H4 Homo sapiens 0.011263230999999999 2 Escherichia coli LEVO SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGFGG P62805 Histone H2A type 1 Homo sapiens 0.013964305

H2A crosslinked at K119C with acetone linker to ubiquitin G76C

2 Escherichia coli LEVO SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKCTESHHKAKGK P0C0S8 Histone H2B type 1-C/E/F/G/I Homo sapiens 0.013806018 2 Escherichia coli LEVO PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRL AHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK P62807 DNA (145-MER) synthetic construct 0.060642589999999996 1 (DG)(DG)(DT)(DG)(DG)(DG)(DC)(DG)(DC)(DG)(DC)(DG)(DA)(DA)(DC)(DT)(DG)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DG)(DC)(DC)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DG)(DG) (DC)(DG)(DT)(DA)(DT)(DG)(DG)(DT)(DG)(DA)(DC)(DA)(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)(DC)(DA) DNA DNA (145-MER) synthetic construct 0.059771035 1 (DT)(DG)(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)(DT)(DG)(DT)(DC)(DA)(DC)(DC)(DA)(DT)(DA)(DC)(DG)(DC)(DC)(DC)(DT)(DA) (DA)(DT)(DT)(DA)(DG)(DA)(DG)(DG)(DC)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DC)(DA) (DG)(DT)(DT)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DC)(DC) DNA DNA (cytosine-5)-methyltransferase 3A Homo sapiens 0.10226973399999999

copurified with DNMT3L

1 Escherichia coli LEVO SNAMPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPVESGDTPKDPAVISKSPS MAQDSGASELLPNGDLEKRSEPQPEEGSPAGGQKGGAPAEGEGAAETLPEASRAVENGCCTPKEGRGAPAEAGKEQKETN IESMKMEGSRGRLRGGLGWESSLRQRPMPRLTFQAGDPYYISKRKRDEWLARWKREAEKKAKVIAGMNAVEENQGPGESQ KVEEASPPAVQQPTDPASPTVATTPEPVGSDAGDKNATKAGDDEPEYEDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTG RSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSAFHQATYNKQPMYRKAIYEVLQVASSRAGKLFPVCHDSDESDTAK AVEVQNKPMIEWALGGFQPSGPKGLEPPEEEKNPYKEVYTDMWVEPEAAAYAPPPPAKKPRKSTAEKPKVKEIIDERTRE RLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRC FCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFANNHDQEFDPPKVYPPVPAEKRKPIRVL SLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVN PARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGN LPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDV SNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV Q9Y6K1 singleParticle particle 0.13 7.5 15.0 C8H18N2O4S HEPES 65.0 NaCl sodium chloride 1.0 C4H10O2S2 Dithiothreitol 0.1 C15H22N6O5S S-Adenosyl methionine

15 mM HEPES pH 7.5, 65 mM NaCl, 1 mM DTT, 0.1 mM S-Adenosyl methionine

Quantifoil R2/2 COPPER 300 CARBON HOLEY GLOW DISCHARGE 90 AIR 0.038 ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 3.0 105000.0 GIF Bioquantum 20 GATAN K3 (6k x 4k) 2 15491 61.0 1 7826521 1 C1 FOURIER SPACE 3.1 FSC 0.143 CUT-OFF cryoSPARC 4.3.1 191397 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 1 191397.0 cryoSPARC 4.3.1 K Other in silico model

Model Angelo

7XD1 PDB experimental model RIGID BODY FIT REAL 50.0 emd_18778_msk_1.map emd_18778_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.336 318.336 318.336 90.0 90.0 90.0 X Y Z -0.29871672 0.85236484 0.00036416895 0.023464002 0.829 0.829 0.829 AUTHOR ::::EMDATABANK.org::::EMD-18778:::: DNMT3A1-DNMt3L-NCP H2AK119ub processed by homogenous refinement with wider mask (map 2) emd_18778_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.336 318.336 318.336 90.0 90.0 90.0 X Y Z -0.2576172 0.69625056 0.00046869132 0.023127696 0.829 0.829 0.829 AUTHOR ::::EMDATABANK.org::::EMD-18778:::: DNMT3A1-DNMt3L-NCP H2AK119ub processed by homogenous refinement with wider mask (map 2) emd_18778_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.336 318.336 318.336 90.0 90.0 90.0 X Y Z -0.6593639 1.3439287 0.0006483252 0.028940195 0.829 0.829 0.829 AUTHOR ::::EMDATABANK.org::::EMD-18778:::: canonical DNMT3A1-DNMt3L-NCP H2AK119ub map sharpened with bfactor -50 emd_18778_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 265.28 265.28 265.28 90.0 90.0 90.0 X Y Z -0.010626575 0.06812412 0.00031941046 0.0035905677 1.658 1.658 1.658 AUTHOR ::::EMDATABANK.org::::EMD-18778:::: DNMT3A1-DNMt3L-NCP H2AK119ub processed in relion with circular mask and offset applied emd_18778_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.336 318.336 318.336 90.0 90.0 90.0 X Y Z -0.43652984 0.9584568 0.0010266069 0.034202646 0.829 0.829 0.829 AUTHOR ::::EMDATABANK.org::::EMD-18778:::: canonical DNMT3A1-DNMt3L-NCP H2AK119ub halfmap 2 emd_18778_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.336 318.336 318.336 90.0 90.0 90.0 X Y Z -0.45583978 0.9920055 0.0010241955 0.034244295 0.829 0.829 0.829 AUTHOR ::::EMDATABANK.org::::EMD-18778:::: canonical DNMT3A1-DNMt3L-NCP H2AK119ub halfmap 1