Cryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor

2026-05-13 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 Model completeness

Lipids were incorporated.

STRUCTURE_SUMMARY atom_site atom_type chem_comp chem_comp_atom chem_comp_bond em_admin em_entity_assembly em_entity_assembly_naturalsource em_imaging em_software entity entity_poly entity_poly_seq entity_src_nat pdbx_contact_author pdbx_entity_instance_feature pdbx_entity_nonpoly pdbx_entry_details pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly pdbx_struct_assembly_gen pdbx_struct_oper_list pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues pdbx_validate_torsion struct_asym struct_conf struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet struct_sheet_order struct_sheet_range _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type _em_admin.last_update _em_entity_assembly.entity_id_list _em_entity_assembly_naturalsource.id _em_imaging.microscope_model _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly_seq.entity_id _entity_poly_seq.mon_id _entity_poly_seq.num _entity_src_nat.pdbx_end_seq_num _entity_src_nat.strain _pdbx_entry_details.has_ligand_of_interest _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id _pdbx_struct_assembly.details _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.sheet_id _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 _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi _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 _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.pdbx_db_accession _struct_ref_seq.pdbx_strand_id _struct_ref_seq.ref_id _struct_ref_seq.seq_align_end _struct_sheet.number_strands _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.sense _struct_sheet_order.sheet_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_seq_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.id _struct_sheet_range.sheet_id STRUCTURE_SUMMARY em_admin em_entity_assembly em_entity_assembly_naturalsource em_imaging em_software entity entity_poly entity_src_nat struct_ref struct_ref_seq struct_ref_seq_dif _chem_comp.name _chem_comp.pdbx_synonyms _em_admin.last_update _em_entity_assembly.entity_id_list _em_entity_assembly_naturalsource.id _em_imaging.microscope_model _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_src_nat.pdbx_end_seq_num _entity_src_nat.strain _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.pdbx_db_accession _struct_ref_seq.pdbx_strand_id _struct_ref_seq.ref_id _struct_ref_seq.seq_align_end DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBj PDBj 2024-04-18 2025-10-22 2025-10-22 2026-05-13 National Natural Science Foundation of China (NSFC) 81925024 China National Natural Science Foundation of China (NSFC) U23A20163 China Ministry of Science and Technology (MoST, China) 2017YFA0503900 China Cryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor Zhang L Tan JX Zhou Y Zhu YQ Polar flagellum, Polar flagellar motor, Proximal rod, MOTOR PROTEIN Zhang L Tan J Duan X Wang X Wang T Yuan K Homma M Kojima S Zhou Y Zhu Y Molecular basis of high-torque transmission of the Vibrio polar flagellar motor. Protein Cell CN 2026 41871453 doi:10.1093/procel/pwag025 1674-8018 8z5s FULLOVERLAP EMDB EMD-39780 associated EM volume

The polar flagellar motor-hook complex The polar flagellar motor-hook complex 0 1 2 3 4 5 6 7 8 9 Vibrio alginolyticus KK148 Flagellar biosynthetic protein FliP Vibrio alginolyticus KK148 0.031314904 5 LEVO MTKGNPIRLLLSTLLLFVGVLFSSFSFAEAEESALPDNLADGSSVTVQAMQSDTGASRAMSVSSGGGIPAFTMTTNPDGS EDYSVTLQILALMTMLGFLPAMVILMTSFTRIVVVMSILRQAMGLQQTPSNQVIIGIALFLTFFVMSPVLNEINDKAVQP YLNEQVTAREAFDAAQAPMKAFMLKQTRIKDLETFVTMSGEQVDNPEDVSMAVLIPAFITSELKTAFQIGFMLFLPFLII DLVVASVLMAMGMMMLSPMIVSLPFKLMLFVLVDGWNLILSTLAGSFAL A0A1W6TTE6 Flagellar biosynthetic protein FliQ Vibrio alginolyticus KK148 0.010329614999999999 4 LEVO MTPEMFVELFREALWMVLIMVCAIIIPSLLIGLIVAIFQAATSINEQTLSFLPRLIVTLLALMLFGHWMTQMLMEYFYGL IERLPQVLY A0A0H0YAF4 Flagellar basal-body rod protein FlgF Vibrio alginolyticus KK148 0.026987386999999998 5 LEVO MDRALFLAMSGAKQNMQALQLRANNLANVSTTGFRADLAQARSMQAYGEGHPSRVFSMTERPGHNFAQGSVITTGRDLDV TIEGSGWISVLDHTGKEGLTRNGNLKVDQNGMLTNASGHLVLGENDAPITLPIPLSKIEIGRDGTISVLPQGAPAEEFQA VDRIKLVKPNDQSLFKDTNGLFRHKTPNQPYEADATVSLQTGAIEGSNVNAVGEMTALIDLQRQFEMQVKMMSTAEEMDK SSDSLLRMS A0A0G9M4M9 Flagellar hook-basal body complex protein FliE Vibrio alginolyticus 0.011135678999999999 6 LEVO MKVDGIQAEMRAMMVEATNTAPTASGAKVGADFNDLLTKAINNVNTLQKASGDLQTRFDRGDADVSLSDVMIARNKSSVA FDATVQIRNKLVEAYKDLMNMPV A0A0H0Y9C1 Flagellar biosynthetic protein FlhB Vibrio alginolyticus KK148 0.042197296999999995 1 LEVO MAESDGQERTEEATPRRLQQAREKGQVARSKELASASVLIVGAISLMWFGEALARSLFSIMSRLFDLQREEIFDTAKLFD IALGAMTDLLFPLFLVLATLFTAAMIGAAGVGGISFSAQAAMPKLSKMNPLSGLKRMVGMQSWVELIKSILKVVLVTGVA IYLIQASQADLIQLSMDVYPQNIFHALDILLNFILLISCSLLIVVAIDIPFQIWQHADQLKMTKQEVKDEYKETEGKPEV KGRIRMLQREAAQRRMMADVPQADVIVTNPEHFSVALRYKQKTDRAPVVIAKGTDHMAMKIREVAREHDITIVPAPPLAR ALYHTTELEQEIPDGLFTAVAQVLAFVFQLKQYRKRGGQRPKIQDYDLPIPPEHRH A0A0H0YB55 Flagellar biosynthetic protein FliR Vibrio alginolyticus KK148 0.028905535 1 LEVO MEYPTSVVLDWIANYFWPYVRISSMLMVMTVTGARFVSPRIRLYLGLAITFAVMPAIPAVPQDIELLSFRGFMTIAEQMI IGIAMGMVTQFMIQTFVLLGQILGMQSSLGFASMVDPANGQNTPLLGQLFMFLTTMFFLATDGHLKMLQLVVFSFKTLPI GSGSLNAVDFREMAGWLGIMFQTALSMSLSGIIALLTINLSFGVMTRAAPQLNIFSLGFAFALMVGLLLCWYILAGLYSH YEMFWTVGEAQICRLIRLEC A0A0H0YFV7 Flagellar M-ring protein Vibrio alginolyticus KK148 0.063915605 15 LEVO MADKSTDLTVTEGGSDGALVASSDVDVESQNPDLEERSASKFDMAVGDLDLLRQVVLVLSISICVALIVMLFFWVKEPEM RPLGAYETEELIPVLDYLDQQKINYKLDGNTISVESSEYNSIKLGMVRSGVNQATEAGDDILLQDMGFGVSQRLEQERLK LSRERQLAQAIEEMKQVRKARVLLALPKHSVFVRHNQEASASVFLTLSTGTNLKQQEVDSIVDMVASAVPGMKTSRITVT DQHGRLLSSGSQDPASAARRKEQELERSQEQALREKIDSVLLPILGYGNYTAQVDIQMDFSAVEQTRKRFDPNTPATRSE YALEDYNNGNMVAGIPGALSNQPPADASIPQDVAQMKDGSVMGQGSVRKESTRNFELDTTISHERKQTGTVARQTVSVAI KDRRQVNPDTGEVTYTPMSESEINAIRQVLIGTVGFDQGRGDLLNVLSVKFAEPEAEQLEEPPIWEHPNFSDWVRWFASA LVIIVVVLVLVRPAMKKLLNPTSDDEDEMYGPDGLPIGADGETSLIGSDIESSELFEFGSSIDLPNLHKDEDVLKAVRAL VANEPELAAQVVKNWMNDNG Q75N27 Flagellar basal body rod protein FlgB Vibrio alginolyticus KK148 0.01423995 5 LEVO MAISFDNALGIHQHTVGVRERNAEVISTNIAQANTPGYKARGLDFAKELQAATSGASIGLSRTDGRHIPATTTLVGDKLY RLPTQPDTGDGNTVDLDLERNLFMQNQIRHQASLDFLGSKFKNLTKAIKGE A0A0G9LZG6 Flagellar basal-body rod protein FlgC Vibrio alginolyticus KK148 0.014812569 6 LEVO MSLFNVFNVTGSAMSAESVRLNTTSSNLANADSVSSSAKDTYKARHAVFGAELSNAMRGGDTVPVKVMGIVESDKPLSAE YNPDHPLANEEGYIYKPNVNVMEEMANMISASRAYQTNVQVADSSKQMLLRTLQMGQ A0A0G9LZH2 (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE 0.000751023 4 PGT (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate 0.0004955869999999999 5 XKP singleParticle particle 8.0 Quantifoil R1.2/1.3 COPPER 300 CARBON CONTINUOUS 200.0 GLOW DISCHARGE 10 ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 1.8 105000.0 TFS Selectris 10 FEI FALCON IV (4k x 4k) 50.0 1 329955 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION C1 3.03 FSC 0.143 CUT-OFF cryoSPARC 58418 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_39780.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 620 620 620 0 0 0 620 620 620 744.0 744.0 744.0 90.0 90.0 90.0 X Y Z -2.095469 2.8748376 -0.0010787722 0.10338749 1.2 1.2 1.2 0.42 AUTHOR ::::EMDATABANK.org::::EMD-39780:::: Main map Other in silico model

ModelAngelo

FLEXIBLE FIT REAL emd_39780_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 620 620 620 0 0 0 620 620 620 744.0 744.0 744.0 90.0 90.0 90.0 X Y Z -1.5510155 2.0054202 -0.000053855587 0.20611106 1.2 1.2 1.2 AUTHOR ::::EMDATABANK.org::::EMD-39780:::: Half map B emd_39780_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 620 620 620 0 0 0 620 620 620 744.0 744.0 744.0 90.0 90.0 90.0 X Y Z -1.5715003 1.9992886 -0.00007666987 0.20609055 1.2 1.2 1.2 AUTHOR ::::EMDATABANK.org::::EMD-39780:::: Half map A