2025-07-02 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation citation_author _citation.pdbx_database_id_PubMed _citation_author.name COORDINATE_REPLACEMENT AUTHOR Sequence discrepancy

The Methionine residues (Met90, Met120) from ChainM and ChainE were replaced with Norleucine (Nle90, Nle120).

STRUCTURE_SUMMARY atom_site atom_site_anisotrop em_software entity entity_poly entity_poly_seq entity_src_gen pdbx_entity_instance_feature pdbx_poly_seq_scheme pdbx_struct_sheet_hbond struct_conf struct_conn struct_ref_seq_dif struct_sheet struct_sheet_order struct_sheet_range _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.group_PDB _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.type_symbol _em_software.category _entity.formula_weight _entity.pdbx_mutation _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly_seq.mon_id _entity_src_gen.pdbx_gene_src_gene _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.comp_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_mon_id DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last _citation.year STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature struct_sheet _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _pdbx_entry_details.has_protein_modification _struct_sheet.number_strands DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name PDBj PDBj 2020-08-14 2020-10-21 2020-10-21 2025-07-02 National Natural Science Foundation of China (NSFC) 31870725 China National Natural Science Foundation of China (NSFC) 31570729 China Other government Fundamental Research Funds for the Central Universities (2017EYT19) China Other government Memorial Sloan-Kettering Cancer Center Core grant P30CA008748 United States National Institutes of Health/National Library of Medicine (NIH/NLM) R01GM079641 United States Other government Basic Research grant from Shenzhen government (JCYJ20180302174213122) China Li W Tian W nucleosome complex, histone methyltransferase, DNA, Gene reguration, GENE REGULATION Li W Tian W Yuan G Deng P Sengupta D Cheng Z Cao Y Ren J Qin Y Zhou Y Jia Y Gozani O Patel DJ Wang Z Nature UK 590 498 503 2021 33361816 doi:10.1038/s41586-020-03069-8 1476-4687 0006 NATUAS EMD-30453 other EM volume EMD-30454 other EM volume EMD-30455 other EM volume 7crq FULLOVERLAP NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) 0 1 2 3 4 5 6 7 0.3 Histone H3, H4, H2A, H2B 1 1 2 3 4 Xenopus laevis DNA 1 5 6 Xenopus laevis NSD3 1 7 Homo sapiens Histone H3 Xenopus laevis 0.015223779 2 Escherichia coli LEVO ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGV(NLE)KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ DFKTDLRFQSSAV(NLE)ALQEASEAYLVGLFEDTNLCGIHAKRVTI(NLE)PKDIQLARRIRGERA Q92133 Histone H4 Xenopus laevis 0.011263230999999999 2 Escherichia coli LEVO SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A Xenopus laevis 0.013978240999999999 2 Escherichia coli LEVO SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK Q6AZJ8 Histone H2B Xenopus tropicalis 0.013524752 2 Escherichia coli LEVO AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHY NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK Q6AZK7 DNA (168-MER) Xenopus laevis 0.057488551 1 (DA)(DT)(DC)(DG)(DG)(DG)(DT)(DG)(DA)(DT)(DG)(DC)(DC)(DC)(DG)(DA)(DT)(DC)(DC)(DC) (DC)(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)(DT)(DC)(DC)(DA)(DG)(DT)(DG)(DC)(DC)(DG)(DG)(DT)(DG) (DT)(DC)(DG)(DC)(DG)(DA)(DT) DNA DNA (168-MER) Xenopus laevis 0.057982917999999994 1 (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC)(DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (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)(DG)(DG)(DG)(DG)(DA)(DT)(DC)(DG)(DG)(DG)(DC)(DA)(DT)(DC) (DA)(DC)(DC)(DC)(DG)(DA)(DT) DNA Histone-lysine N-methyltransferase NSD3 Homo sapiens 0.085454359 2 Baculovirus transfer vector pFASTBAC1 LEVO VSDVQSMDSSLSRRGTGMSKKDTVCQICESSGDSLIPCEGECCKHFHLECLGLASLPDSKFICMECKTGQHPCFSCKVSG KDVKRCSVGACGKFYHEACVRKFPTAIFESKGFRCPQHCCSACSMEKDIHKASKGRMMRCLRCPVAYHSGDACIAAGSML VSSYILICSNHSKRSSNSSAVNVGFCFVCARGLIVQDHSDPMFSSYAYKSHYLLNESNRAELMKLPMIPSSSASKKKCEK GGRLLCCESCPASFHPECLSIEMPEGCWNCNDCKAGKKLHYKQIVWVKLGNYRWWPAEICNPRSVPLNIQGLKHDLGDFP VFFFGSHDYYWVHQGRVFPYVEGDKSFAEGQTSINKTFKKALEEAAKRFQELKAQRESKEALEIEKNSRKPPPYKHIKAN KVIGKVQIQVADLSEIPRCNCKPADENPCGLESECLNRMLQYECHPQVCPAGDRCQNQCFTKRLYPDAEIIKTERRGWGL RTKRSIKKGEFVNEYVGELIDKEECRLRIKRAHENSVTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCEAQKWTVNG DVRVGLFALCDIPAGMELTFNYNLDCLGNGRTECHCGADNCSGFLGVRPKSACASTNEEKAKNAKLKQKRRKIKTEPKQM HEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSAL EGRLCCSEHDPMAPVSPEYWSKIKCKWESQDHGEEVKE Q9BZ95 2.1.1.- S-ADENOSYLMETHIONINE 0.000398437 2 SAM ZINC ION 6.5409e-05 6 ZN singleParticle particle 0.3 7.5 ETHANE 100 281 FEI VITROBOT MARK IV

blotted for 3 s before being plunged into liquid ethane.

The sample was monodisperse.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.15 FSC 0.143 CUT-OFF 281815 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD