CryoEM structure of the human Separase-Securin complex

2025-10-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY SOURCE_AND_TAXONOMY em_admin em_imaging em_software entity_src_gen _em_admin.last_update _em_imaging.microscope_model _entity_src_gen.gene_src_common_name STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update COORDINATE_REPLACEMENT AUTHOR Model completeness

We have got a 3.45 A-resolution map of the N-terminal Heat-repeat domain of separase, we then revisited the securin-separase structure (this entry) and found the N-terminal domain in the model could be improved. With the guidance of high-resolution map of separase and Alphafold3-predicted structure of full-length securin-separase complex, we re-built the N-terminal domain of separase (aa 248-442) and securin (aa 154-163).

STRUCTURE_SUMMARY atom_site em_admin em_imaging em_software entity_src_gen pdbx_contact_author pdbx_poly_seq_scheme pdbx_struct_oper_list pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues pdbx_validate_torsion refine_ls_restr software struct_conf _em_admin.last_update _em_imaging.microscope_model _entity_src_gen.gene_src_common_name _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_struct_oper_list.symmetry_operation _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_seq_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_seq_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_seq_id _struct_conf.end_label_asym_id _struct_conf.end_label_comp_id _struct_conf.end_label_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.pdbx_PDB_helix_length PDBe PDBe 2021-02-14 2021-08-04 2021-08-04 2025-10-01 Swiss National Science Foundation 310030_185235 Switzerland National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35-GM118053 United States CryoEM structure of the human Separase-Securin complex Yu J Raia P pseudosubstrate HEAT repeat caspase cell cycle, HYDROLASE Yu J Raia P Ghent CM Raisch T Sadian Y Cavadini S Sabale PM Barford D Raunser S Morgan DO Boland A Structural basis of human separase regulation by securin and CDK1-cyclin B1. Nature UK 596 138 142 2021 34290405 doi:10.1038/s41586-021-03764-0 1476-4687 0006 NATUAS 7nj1 FULLOVERLAP EMDB EMD-12369 associated EM volume

Inhibitory complex of human separase bound to securin. Inhibitory complex of human separase bound to securin. 0 1 2 Homo sapiens Separin Homo sapiens 0.237610469 1 Spodoptera frugiperda LEVO MRSFKRVNFGTLLSSQKEAEELLPDLKEFLSNPPAGFPSSRSDAERRQACDAILRACNQQLTAKLACPRHLGSLLELAEL ACDGYLVSTPQRPPLYLERILFVLLRNAAAQGSPEVTLRLAQPLHACLVQCSREAAPQDYEAVARGSFSLLWKGAEALLE RRAAFAARLKALSFLVLLEDESTPCEVPHFASPTACRAVAAHQLFDASGHGLNEADADFLDDLLSRHVIRALVGERGSSS GLLSPQRALCLLELTLEHCRRFCWSRHHDKAISAVEKAHSYLRNTNLAPSLQLCQLGVKLLQVGEEGPQAVAKLLIKASA VLSKSMEAPSPPLRALYESCQFFLSGLERGTKRRYRLDAILSLFAFLGGYCSLLQQLRDDGVYGGSSKQQQSFLQMYFQG LHLYTVVVYDFAQGCQIVDLADLTQLVDSCKSTVVWMLEALEGLSGQELTDHMGMTASYTSNLAYSFYSHKLYAEACAIS EPLCQHLGLVKPGTYPEVPPEKLHRCFRLQVESLKKLGKQAQGCKMVILWLAALQPCSPEHMAEPVTFWVRVKMDAARAG DKELQLKTLRDSLSGWDPETLALLLREELQAYKAVRADTGQERFNIICDLLELSPEETPAGAWARATHLVELAQVLCYHD FTQQTNCSALDAIREALQLLDSVRPEAQARDQLLDDKAQALLWLYICTLEAKIQEGIERDRRAQAPGNLEEFEVNDLNYE DKLQEDRFLYSNIAFNLAADAAQSKCLDQALALWKELLTKGQAPAVRCLQQTAASLQILAALYQLVAKPMQALEVLLLLR IVSERLKDHSKAAGSSCHITQLLLTLGCPSYAQLHLEEAASSLKHLDQTTDTYLLLSLTCDLLRSQLYWTHQKVTKGVSL LLSVLRDPALQKSSKAWYLLRVQVLQLVAAYLSLPSNNLSHSLWEQLCAQGWQTPEIALIDSHKLLRSIILLLMGSDILS TQKAAVETSFLDYGENLVQKWQVLSEVLSCSEKLVCHLGRLGSVSEAKAFCLEALKLTTKLQIPRQCALFLVLKGELELA RNDIDLCQSDLQQVLFLLESCTEFGGVTQHLDSVKKVHLQKGKQQAQVPCPPQLPEEELFLRGPALELVATVAKEPGPIA PSTNSSPVLKTKPQPIPNFLSHSPTCDCSLCASPVLTAVCLRWVLVTAGVRLAMGHQAQGLDLLQVVLKGCPEAAERLTQ ALQASLNHKTPPSLVPSLLDEILAQAYTLLALEGLNQPSNESLQKVLQSGLKFVAARIPHLEPWRASLLLIWALTKLGGL SCCTTQLFASSWGWQPPLIKSVPGSEPSKTQGQKRSGRGRQKLASAPLSLNNTSQKGLEGRGLPCTPKPPDRIRQAGPHV PFTVFEEVCPTESKPEVPQAPRVQQRVQTRLKVNFSDDSDLEDPVSAEAWLAEEPKRRGTASRGRGRARKGLSLKTDAVV APGSAPGNPGLNGRSRRAKKVASRHCEERRPQRASDQARPGPEIMRTIPEEELTDNWRKMSFEILRGSDGEDSASGGKTP APGPEAASGEWELLRLDSSKKKLPSPCPDKESDKDLGPRLQLPSAPVATGLSTLDSICDSLSVAFRGISHCPPSGLYAHL CRFLALCLGHRDPYATAFLVTESVSITCRHQLLTHLHRQLSKAQKHRGSLEIADQLQGLSLQEMPGDVPLARIQRLFSFR ALESGHFPQPEKESFQERLALIPSGVTVCVLALATLQPGTVGNTLLLTRLEKDSPPVSVQIPTGQNKLHLRSVLNEFDAI QKAQKENSSCTDKREWWTGRLALDHRMEVLIASLEKSVLGCWKGLLLPSSEEPGPAQEASRLQELLQDCGWKYPDRTLLK IMLSGAGALTPQDIQALAYGLCPTQPERAQELLNEAVGRLQGLTVPSNSHLVLVLDKDLQKLPWESMPSLQALPVTRLPS FRFLLSYSIIKEYGASPVLSQGVDPRSTFYVLNPHNNLSSTEEQFRANFSSEAGWRGVVGEVPRPEQVQEALTKHDLYIY AGHGAGARFLDGQAVLRLSCRAVALLFGCSSAALAVHGNLEGAGIVLKYIMAGCPLFLGNLWDVTDRDIDRYTEALLQGW LGAGPGAPLLYYVNQARQAPRLKYLIGAAPIAYGLPVSLRSSLAEENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK Q14674 3.4.22.49 Securin Homo sapiens 0.02205234 1 Spodoptera frugiperda LEVO MATLIYVDKENGEPGTRVVAKDGLKLGSGPSIKALDGRSQVSTPRFGKTFDAPPALPKATRKALGTVNRATEKSVKTKGP LKQKQPSFSAKKMTEKTVKAKSSVPASDDAYPEIEKFFPFNPLDFESFDLPEEHQIAHLPLSGVPLMILDEERELEKLFQ LGPPSPVKMPSPPWESNLLQSPSSILSTLDVELPPVCCDIDI O95997 singleParticle particle 0.025 7.8 Quantifoil R1.2/1.3 GOLD 300 GRAPHENE OXIDE CONTINUOUS GLOW DISCHARGE ETHANE 90 293 LEICA EM GP

The sample was monodisperse. We use graphene oxide-coated EM grids.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 1.3 1.3 2.5 2.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 4 16540 3.0 67.0 1 CTFFIND Gctf cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION C1 2.9 FSC 0.143 CUT-OFF RELION 205300 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_12369.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 318 318 318 0 0 0 318 318 318 333.9 333.9 333.9 90.0 90.0 90.0 X Y Z -0.028123753 1.8777864 0.0007226745 0.017121399 1.05 1.05 1.05 0.1 AUTHOR ::::EMDATABANK.org::::EMD-12369:::: Postprocessed map of human Separase-Securin complex at 2.9A. AB INITIO MODEL emd_12369_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 318 318 318 0 0 0 318 318 318 333.9 333.9 333.9 90.0 90.0 90.0 X Y Z -0.032967232 0.080295146 0.00010927322 0.0013865392 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-12369:::: Focus-refined map (unsharpened) of human Separase-Securin complex at 2.9A. emd_12369_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 318 318 318 0 0 0 318 318 318 333.9 333.9 333.9 90.0 90.0 90.0 X Y Z -0.030897772 1.7817645 0.00060843345 0.016638307 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-12369:::: Focus-refined map (postprocessed) of human Separase-Securin complex at 2.9A. emd_12369_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 318 318 318 0 0 0 318 318 318 333.9 333.9 333.9 90.0 90.0 90.0 X Y Z -0.03168577 0.07737534 0.00015176105 0.001433202 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-12369:::: Unsharpened map of human Separase-Securin complex at 2.9A.