Clostridium perfringens iota toxin pore Ib in prepore V state

2026-09-09 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Atoms with unrealistic or zero occupancies STRUCTURE_SUMMARY atom_site em_admin entity entity_poly entity_poly_seq entity_src_gen pdbx_contact_author pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_conn_angle pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues pdbx_validate_torsion refine refine_ls_restr struct_conf struct_conn struct_mon_prot_cis struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet struct_sheet_order struct_sheet_range _em_admin.last_update _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _refine.ls_d_res_high _refine.pdbx_stereochemistry_target_values _refine_ls_restr.dev_ideal _refine_ls_restr.number _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_omega_angle _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.seq_align_end STRUCTURE_SUMMARY em_admin entity entity_poly entity_src_gen struct_ref struct_ref_seq struct_ref_seq_dif _em_admin.last_update _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.seq_align_end PDBj PDBj 2024-09-30 2025-05-14 2025-05-14 2026-09-09 Japan Society for the Promotion of Science (JSPS) 21J13410 Japan Japan Society for the Promotion of Science (JSPS) 21H02452 Japan Japan Society for the Promotion of Science (JSPS) 24K01993 Japan Japan Agency for Medical Research and Development (AMED) 2366 Japan Clostridium perfringens iota toxin pore Ib in prepore V state Yamada T Sugita Y Yoshida T Noda T Tsuge H Toxin, Prepore, Pre-pore, Pore, Translocation Yamada T Sugita Y Yoshida T Noda T Tsuge H Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis To Be Published 0353 9jsl FULLOVERLAP EMDB EMD-61776 associated EM volume

Clostridium perfringens iota toxin component Ib Clostridium perfringens iota toxin component Ib 0 1 Clostridium perfringens NCIB 10748 Iota toxin component Ib Clostridium perfringens NCIB 10748 0.058754531 7 Escherichia coli BL21(DE3) LEVO EDLDTDNDNIPDAYEKNGYTIKDSIAVKWNDSFAEQGYKKYVSSYLESNTAGDPYTDYQKASGSIDKAIKLEARDPLVAA YPVVGVGMENLIISTNEHASSDQGKTVSRATTNSKTDANTVGVSISAGYQNGFTGNITTSYSHTTDNSTAVQDSNGESWN TGLSINKGESAYINANVRYYNTGTAPMYKVTPTTNLVLDGETLATIKAQDNQIGNNLSPNETYPKKGLSPLALNTMDQFN ARLIPINYDQLKKLDSGKQIKLETTQVSGNYGTKNSQGQIITEGNSWSNYISQIDSVSASIILDTGSQTFERRVAAKEQG NPEDKTPEITIGEAIKKAFSATKNGELLYFNGIPIDESCVELIFDDNTSEIIKEQLKYLDDKKIYNVKLERGMNILIKVP SYFTNFDEYNNFPASWSNIDTKNQDGLQSVANKLSGETKIIIPMSKLKPYKRYVFSGYSKDPSTSNSITVNIKSKEQKTD YLVPEKDYTKFSYEFETTGKDSSDIEITLTSSGVIFLDNLSITELNSTPEIL Q46221 CALCIUM ION 4.0078e-05 21 CA singleParticle particle 8.0 20.0 C4H11NO3 tris hydroxymethyl aminomethane 100.0 NaCl Sodium Chloride 1.0 CaCl2 Calcium Chloride Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.01 0.6 1.6 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 1 11549 50.0 1 6223563 cryoSPARC 3.3.2 patch CTF estimation PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-0721 C1 3.59 FSC 0.143 CUT-OFF cryoSPARC 3.3.2 11285 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 emd_61776.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 216 216 216 0 0 0 216 216 216 190.08 190.08 190.08 90.0 90.0 90.0 X Y Z -0.43003523 0.97715265 0.011668787 0.08427097 0.88 0.88 0.88 0.24 AUTHOR ::::EMDATABANK.org::::EMD-61776:::: 6klx ABCD PDB experimental model Q46221 EFG AlphaFold in silico model REAL emd_61776_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 216 216 216 0 0 0 216 216 216 190.08 190.08 190.08 90.0 90.0 90.0 X Y Z -6.0099583 8.034185000000001 0.025571825 0.3225595 0.88 0.88 0.88 AUTHOR ::::EMDATABANK.org::::EMD-61776:::: emd_61776_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 216 216 216 0 0 0 216 216 216 190.08 190.08 190.08 90.0 90.0 90.0 X Y Z -2.1753604 2.5038464 0.012674958 0.41464067 0.88 0.88 0.88 AUTHOR ::::EMDATABANK.org::::EMD-61776:::: emd_61776_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 216 216 216 0 0 0 216 216 216 190.08 190.08 190.08 90.0 90.0 90.0 X Y Z -2.1446638 2.6143317 0.012641886 0.41326138 0.88 0.88 0.88 AUTHOR ::::EMDATABANK.org::::EMD-61776::::