Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_validate_close_contact struct_conn struct_ref struct_ref_seq struct_ref_seq_dif _em_admin.last_update _pdbx_entry_details.has_protein_modification _struct_ref.db_code _struct_ref.db_name _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _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_db_accession _struct_ref_seq.seq_align_beg EXPERIMENTAL_SUMMARY em_admin struct_ref struct_ref_seq struct_ref_seq_dif _em_admin.last_update _struct_ref.db_code _struct_ref.db_name _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _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_db_accession _struct_ref_seq.seq_align_beg REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_validate_chiral pdbx_validate_close_contact struct_conn _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight PDBe PDBe 2023-04-25 2024-07-17 2024-07-17 2026-09-02 Knut and Alice Wallenberg Foundation KAW 2019.0043 Sweden Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis Kovalova T Krol S Sjostrand D Riepl D Gamiz-Hernandez A Brzezinski P Kaila V Hogbom M RESPIRATORY SUPERCOMPLEX, MEMBRANE PROTEIN, ACTINOBACTERIA, ELECTRON TRANSPORT Riepl D Gamiz-Hernandez AP Kovalova T Krol SM Mader SL Sjostrand D Hogbom M Brzezinski P Kaila VRI Long-range charge transfer mechanism of the III 2 IV 2 mycobacterial supercomplex. Nat Commun UK 15 5276 5276 2024 38902248 doi:10.1038/s41467-024-49628-9 2041-1723 8ovc FULLOVERLAP EMDB EMD-17210 associated EM volume

The respiratory supercomplex The respiratory supercomplex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Mycolicibacterium smegmatis Cytochrome bc1 complex cytochrome c subunit Mycolicibacterium smegmatis 0.029109944999999998 2 Mycolicibacterium smegmatis LEVO MHHHHHHMGSMTSKSRRRLRRRLSAGLLLLIGLAVAGGVAATLTPQPQVAVADESQSALLRTGKQLFETSCVSCHGANLQ GVPDRGPSLIGTGEAAVYFQVSTGRMPAMRGEAQAPSKPPHFDESQIDALGAYVQANGGGPTVPRDDHGAVAQESLIGGD VARGGDLFRLNCASCHNFTGKGGALSSGKYAPDLGDANPAQIYTAMLTGPQNMPKFSDRQLTPDEKRDIVAYVRESAETP SYGGYGLGGFGPAPEGMAMWIIGMVAAIGVAMWIGSRA A0R050 7.1.1.8 Cytochrome bc1 complex cytochrome c subunit Mycolicibacterium smegmatis 0.04486939499999999 2 Mycolicibacterium smegmatis LEVO MDRIASMSQDSPDIKGTDAPGQTGVPGQPTDAELAEMSREELVKLGGKIDGVETIFKEPRWPVPGTKAEKRTERLVAYWL MLGGLSGLALLLVFLFWPWEYQPFGSEGEFLYSLATPLYGLTFGLSILSIGIGAVLFQKKFIPEEISVQDRHDGRSPEVH RKTVAANLTDALEGSTLKRRKVIGLSLGIGLGAFGAGTLVAFIGGLIKNPWKPVVPTAEGKKAVLWTSGWTPRFKGETIY LARATGRPGESPFVKMRPEDIDAGGMETVFPWRESDGDGTTVESEHKLTEIAMGVRNPVMLIRIKPADMHRVIKRKGQES FNFGELFAYTKVCSHLGCPSSLYEQQTYRILCPCHQSQFDALEFAKPIFGPAARALAQLPITIDEDGYLVANGDFVEPVG PAFWERKS A0R051 7.1.1.8 Cytochrome bc1 complex cytochrome b subunit Mycolicibacterium smegmatis 0.061514281 2 Mycolicibacterium smegmatis LEVO MSPDFAKLAAAQGDAIDSRYHPSAAVRRQLNKVFPTHWSFLLGEIALYSFIILLLTGVWLTLFFDPSMAHVTYDGVYQPL RGVQMSRAYETALDISFEVRGGLFVRQVHHWAALMFAASIMVHLARIFFTGAFRRPREANWVIGSLLLILAMFEGFFGYS LPDDLLSGTGIRAALSGITMGIPVIGTWMHWALFGGDFPGEILIPRLYALHILLIPGIILALIGAHLALVWFQKHTQFPG PGRTETNVVGVRVMPVFAVKSGAFFAMITGVLGLMGGLLTINPIWNLGPYKPSQVSAGSQPDFYMMWTDGLIRLWPAWEF YPFGHTIPQGVWVAVGMGLVFALLIAYPFIEKKVTGDDAHHNLLQRPRDVPVRTAIGSMAIALYLLLTFACMNDIIALKF HISLNATTWIGRIGMVVLPAIVYFVAYRWAISLQRSDREVLEHGVETGIIKRLPHGAYVELHQPLGPVDEHGHPIPLEYA GAPLPKRMNKLGSGGAPGTGSFLFPDPAVEHEALTEAAHASEHKSLTALKEHQDRIHGNGETNGHHKLDYKDDDDK A0R052 7.1.1.8 Transmembrane protein Mycolicibacterium smegmatis 0.011329908999999999 2 Mycolicibacterium smegmatis LEVO MSSTQDRSQLDPEEQPVANTEVERHTGVDVEDVPSAEWGWSHMPIGVMHIGGLLSAAFLLVMMRGNHVGHVEDWFLIGFA AVIVALVGRNWWLRRRGWIR Probable cytochrome c oxidase subunit 3 Mycolicibacterium smegmatis 0.022196883 2 Mycolicibacterium smegmatis LEVO MTSAVGTSGTAITSRVHSLNRPNMVSVGTIVWLSSELMFFAGLFAMYFTARAQAGGAWPPEPTELNLALAVPVTLVLIAS SFTCQMGVFAAERGDVFGLRRWYVITFLMGLFFVLGQGYEYIHLVEHGTTIPGSAYGSVFYLATGFHGLHVIGGLVAFVL LLARTKMSKFTPAQATAAIVVSYYWHFVDIVWIALFATIYFVR A0R049 Cytochrome c oxidase polypeptide 4 Mycolicibacterium smegmatis 0.015177424 2 Mycolicibacterium smegmatis LEVO MHIEARLFEILTAFFALAAVVYAVLTAMFATGGVEWAGTTALVLTTGLTLITGTFFRFVARRLDTRPEDYEDAEISDGAG ELGFFAPHSWWPILISLSFSTAAVGAALWLPWLIAAGVAFVITSVCGLVFEYYWGPEKH A0R056 7.1.1.9 Cytochrome c oxidase subunit 1 Mycolicibacterium smegmatis 0.06416296499999999 2 Mycolicibacterium smegmatis LEVO MVAEAPPIGELEARRPFPERMGPKGNLIYKLITTTDHKLIGIMYCVVCFAFFLVGGLMALFMRTELAMPGLQFLSNEQFN QLFTMHGTVMLLFYATPIVFGFANLVLPLQIGAPDVAFPRLNALSFWLFLFGALIAIAGFITPGGAADFGWTAYSPLTDA IHSPGAGGDLWIMGLAVGGLGTILGGVNMITTVVCMRAPGMTMFRMPIFTWNILVTSILVLIAFPILTAALFGLAADRHL GAHIYDPANGGVLLWQHLFWFFGHPEVYIIALPFFGIVSEIFPVFSRKPIFGYTTLIYATLAIAALSVAVWAHHMYATGA VLLPFFSFMTFLIAVPTGIKFFNWIGTMWKGQLTFETPMLFSVGFLITFLLGGLSGVLLASPPLDFHVTDSYFVIAHFHY VLFGTIVFATYAGIYFWFPKMTGRLLDERLGKLHFWLTFIGFHTTFLVQHWLGDEGMPRRYADYLPTDGFTTLNVISTVG AFILGVSMLPFVWNVFKSWRYGEPVTVDDPWGYGNSLEWATSCPPPRHNFTELPRIRSERPAFELHYPHMVERMRAEAHV GRAHHPELETADKSS 7.1.1.9 cytochrome-c oxidase Mycolicibacterium smegmatis 0.038077465 2 Mycolicibacterium smegmatis LEVO MTPRGFRVVALSIVLGGSALLLSGCSWSDALALGWPTGITPEAKLNRELWIGSVIASFAVGAIVWGLIFWTSAFHRKKAT DTELPRQFGYNMPLELTLTVIPFLIISVLFYFTVVVQERMMHKDPNPEVVIDVTAFQWNWKFGYQKIAFADGSFDYDGAD PERKEAMTSRPEGKDEHGIEKVGPIRGMTPEDRTYLNFDKIETLGTSSEIPVLVLPAGKRIEFVLNSADVIHGFWVPEFL FKRDVLPEPKANNSDNVFQVSEIQQTGAFVGRCTEMCGTFHAMMNFEVRVVEPNDFKAYIDQRNAGKTNAEALAAINQPP LAITTEPFESRRGELVPQASK A0R057 7.1.1.9 Cytochrome c oxidase subunit Mycolicibacterium smegmatis 0.008365549 2 Mycolicibacterium smegmatis LEVO MSTALTHGLIGGVPLVLFAVLALIFLTRKGPHPDTYKMSDPWTHAPILWAAEEPREHGHGGHGHDSHGVVIGGGASGKW A0R1B6 Uncharacterized protein MSMEG_4692/MSMEI_4575 Mycolicibacterium smegmatis 0.015910971 2 Mycolicibacterium smegmatis LEVO MASGDIATVANAELDLPYGSALTSSGRISAVTEPGELSVHYPFPTMDLVVLDDALKYGSRAAKARFAVYIGPLGADTAAT AREILANVPTPENAVLLAVSPDQRAIEVVYGADVKGRGIESAAPLGVSAAAASFKEGNLIDGLISAVRVMSAGVSPA A0R1B5 LpqE protein Mycolicibacterium smegmatis 0.019118969 2 Mycolicibacterium smegmatis LEVO MNRFSSRAGLAVCGLATAVALTACSAGQISQTTTQEPAVNGVNAQAGQVSLRNVHLRAPQQTDYVEPGTTVELLFVAAND STEGSNKLKSITSDVGEVTLTGDSTVPADGVLIVGEPDGQIQAVENAEAADAVTAEVELTKPITNGLLYDFTFTFEDGET TVAVPISAGEQPRRPVPPAGPGSSEH A0R562 Superoxide dismutase [Cu-Zn] Mycolicibacterium smegmatis 0.023232375 2 Mycolicibacterium smegmatis LEVO MLKPVSVAVLFATPVLALSACSPPGETASSEPGTTPAIWTGSPSPAAPSGEDHGGGHGAGAAGAGETLTAELKTADGTSV ATADFQFADGFATVTIETTTPGRLTPGFHGVHIHSVGKCEANSVAPTGGAPGDFNSAGGHFQVSGHSGHPASGDLSSLQV RADGSGKLVTTTDAFTAEDLLDGAKTAIIIHEKADNFANIPPERYQQVNGAPGPDQTTMATGDAGSRVACGVISAG A0QQQ1 1.15.1.1 Co-purified unknown peptide Mycolicibacterium smegmatis 0.000869063 2 Mycolicibacterium smegmatis LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) Co-purified unknown peptide Mycolicibacterium smegmatis 0.002145636 2 Mycolicibacterium smegmatis LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) HEME C 0.0006205189999999999 4 HEC MENAQUINONE-9 0.0007852329999999999 10 MQ9 acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2) 0.0014158019999999999 4 WUO FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate 0.000853112 4 9YF PROTOPORPHYRIN IX CONTAINING FE 0.000616487 4 HEM CARDIOLIPIN 0.0014640429999999997 16 CDL (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate 0.000564732 3 7PH HEME-A 0.000852837 4 HEA COPPER (II) ION 6.354599999999999e-05 6 CU MAGNESIUM ION 2.4305e-05 2 MG CALCIUM ION 4.0078e-05 2 CA (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate 0.0005949919999999999 4 9XX PALMITIC ACID 0.00025642399999999994 4 PLM water 1.8015e-05 249 HOH singleParticle particle 7.4 Quantifoil R2/2 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK III FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.4 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 QUANTUM (4k x 4k) 48.2 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 6ADQ C1 2.8 FSC 0.143 CUT-OFF cryoSPARC 3.v 90918 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_17210.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 540 540 540 0 0 0 540 540 540 457.056 457.056 457.056 90.0 90.0 90.0 X Y Z -0.82992053 1.5094972 0.000112456735 0.037285727 0.8464 0.8464 0.8464 0.194 AUTHOR ::::EMDATABANK.org::::EMD-17210:::: emd_17210_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 540 540 540 0 0 0 540 540 540 457.056 457.056 457.056 90.0 90.0 90.0 X Y Z -0.6230394 1.0719403 0.00080742687 0.08711914 0.8464 0.8464 0.8464 AUTHOR ::::EMDATABANK.org::::EMD-17210:::: emd_17210_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 540 540 540 0 0 0 540 540 540 457.056 457.056 457.056 90.0 90.0 90.0 X Y Z -0.6429107 1.1870925 0.00081074855 0.087460265 0.8464 0.8464 0.8464 AUTHOR ::::EMDATABANK.org::::EMD-17210::::