Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase

2025-10-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY database_2 em_admin entity _chem_comp.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _entity.formula_weight _entity.pdbx_description STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond database_2 em_admin entity pdbx_entity_nonpoly pdbx_entry_details pdbx_modification_feature pdbx_unobs_or_zero_occ_atoms _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_atom_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.mon_nstd_flag _chem_comp.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.name _pdbx_entry_details.has_protein_modification _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_validate_close_contact struct_conn struct_conn_type _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2020-04-14 2020-09-30 2020-09-30 2025-10-01 Swedish Research Council NT_2015-04107 Sweden European Research Council (ERC) ERC-2018-StG-805230 Sweden Knut and Alice Wallenberg Foundation 2018.0080 Sweden Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - Fo-subcomplex Kock Flygaard R Muhleip A mitochondria, ATP synthase, Fo-subcomplex, IF1 dimer, MEMBRANE PROTEIN Flygaard RK Muhleip A Tobiasson V Amunts A Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization. Nat Commun UK 11 5342 5342 2020 33093501 doi:10.1038/s41467-020-18993-6 2041-1723 6ynx FULLOVERLAP EMDB EMD-10859 associated EM volume

Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - Fo-subcomplex

Mitochondrial ATP synthase, Fo-subcomplex Mitochondrial ATP synthase, Fo-subcomplex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Tetrahymena thermophila subunit a Tetrahymena thermophila 0.052561461000000004 2 LEVO MGRENVLPVHNDVYEDFVFTTPYFQPESTFKSVPKLFSDILLGGVEWVYTTSESVLAYDYKLWYLWSGVSNLDESFDMFF NQYWALSLSTSVFQLFYAVILDRYLSVLFQNTPYTNDWFRMMLHSKETALIWLYHPELSWHINGLNQFFTYFYGGILEFV YFDKSNPDMCILVHTLWIHLLILFLIFTGFVTILFSFYGNPNTEENTIDSDYLAASGTVEAEKEITSIDDYLGLVFAIAY VFGVFFYVHGWTSMLSHAVLLLSCYSIIIMFLFILGMPTLLLYDFGIFFLAYLKGAGKYISSVAEMMFDYTACLVFYIRI LAQWIRVVLMVVTFISLSHYVSDFDITNSALIGSENQSDSMNELNTNFSMTYYILTVLPGKFIYWIYEILHTFFVVCSQF VAFFAIVFWLFLFLYTFFIIEKHEDFFSKKREERKKKLKELWNLKN Q951C1 subunit b Tetrahymena thermophila 0.043910102 2 LEVO MHSTLRVFTKNNCLSFTNMNRFSTAAQVAQANYSKFRADYSASVAAFQQRIKTIEKENTGSMKKPMAKAYEHPYNSEHHP LNFSAVKIAETFHDFIGPEQVSPHYESFAMSRKFLLTFWGGFFVLNFGMATVDLNWIMKSTYIPWIFWFQLMYFYVEGKN SMFMPLLQRFYRRAAANEIFTMEAFYHENIENKLRNLMRITKGQLEYWDIHTSYGEIRADSINNFLANEYLRLQSHITSR ALNILKQAQAYETMNQAALLQKLIDDATSAIDNALKGDKKAEVLARSLDSAIDGLSKGYMDYQNDPLLPLILSSIEANVK KITTLSAQEQANLIGLTAEQLKSIKENDVRARKEFLESQPKLDNNLKNIESVKKILATWGK I7MJ84 subunit d Tetrahymena thermophila 0.026747951 2 LEVO MSMLAKIAKNVVKTQALKNTTAAQTPSFQAPGNQDKILKWISTLSNKATTGESRSYCTQLSSLVSFYNKQHVEQIPTIDF NEWKSVISTQGLVDKVKENYESLIKEQYNTDAISKQISSASSKALDDIENELSFHAAIWLNAYADYTMFLFELEEYNDPN DYLMHENFDFFRGLETELEELTETHNYIPGAKDDVNLRGYLATQFAWGKKVISFYRHPADDFKCAKATKNMLGR Q239R1 subunit f Tetrahymena thermophila 0.024265398 2 LEVO MSLHEKMQTDYLWVKDHSQADSWAKARTHGYNYIAHTVPNKKERYEMIWRSMGKSTDWELEKFRLGKKFPDRGNKRRWFK NLFRLIKNPMGYIFWKTYKARLAKPSLIVTSMFIGFTLGFIKLKAQSIAYSKKQYATLRAGKNIEGSGQVHFGYHDQKWG MPAIPMFQLMYYELPGNSIVVNPCRNQNYRLYFEMRKKLGILPA Q24I07 subunit i/j Tetrahymena thermophila 0.024395543 2 LEVO MNPIQKAWLKILEPVSYVINEKMAKRTGIIGKLGRFFAIGPREYGVHPINRMFIFMNRKYMAFQAVALHRYSFVKSLTHN GFHMLRVFRHFAFVLPATVLAGLGLFVYWGDDNKCYSPDRFPYLKKRAGDMALPLNSLNQRTSAHYIEINAIYGAEMMKR YHKVWENIIEERSKATDQEKKTRYAHPSYQYSPLPVVSIPNVLNPLNLQ I7LZW2 subunit k Tetrahymena thermophila 0.020963871 2 LEVO MWYKYFSKQSWNLRVWRKANLKYNQDDFGMTQPKYIARFGDFRFRLVRTEGALRGCMFFVGFGCFSIINYLYGRYGYIIN ESSQKRAAQDLLDNDMAADKILFKNRVGAPTRPLRSLDDMMAFLSGSATYDQLADYASYNHAMDVNQDQQAGLDSWMSEK DKNMVKYYQRSLGKKVEGI I7LSX6 subunit 8 Tetrahymena thermophila 0.012299237999999999 2 LEVO MITILDYLFLLDLNDDLTRKAVFEQVIIFIFIYCTMNFLAWSTVVELIWPTHFFNRRHSSSQEFIRFRTYTEVLLKISAY NDFFYVLNNYYYNQKLILKN Q950Y8 ATPTT3 Tetrahymena thermophila 0.034719633 2 LEVO MINRSTAFISKNLRQANLTQSSLAMKTQYNQMGFSSDNPYNKRWEYKWKHSYYTYPRDYEHTEVRKPQDSKDVPPIYFAY YKDFVDRWLPGMNMWWQRRHRIFDKFNVYFLPGMSLFFYQFADLALGFKIMAAFPLFLAYTRIRDKTLDPDFKETYLRDM IYQNPEITKYFNEETIHVLDYEFEYLPGYLCPEKFPEYQNKTWQFFNTDTAQAEGFFKFGDVESGATMTLKFKTMPIPGK FRYQVGEPFYFYDLRAEIKCDGVYKEVVLVDEKESLKKIRPFLFLI I7M8Q3 ATPTT4 Tetrahymena thermophila 0.032484051 2 LEVO MQQRKKIYLRQKRKIYIQLKNKEKKKNNQFIQKREKMGYKIRNKSIFWTRAGWKNNWHPKNFNAPRPSYGEFTMGIRCRN DHHSFLRYVQTYRNMSRHCKQYFLGDKQLEETFILGLRSLFLVPYDSQCLTDQIKHGGERRFVDQLDRDFELISYNTHPY QLFTYTVRNEHLAWKNEQYEKIQKGEKTFEQELLDYLDEQVLAEKAKLRDGQNFSIERMTEIALHVFRKARAGKVRPAQD VRGPDGNVNDFLEQRRPFEHPNPTGVTH I7MCZ0 ATPTT5 Tetrahymena thermophila 0.031674639 2 LEVO MSENKAPGQIYAYDIHNTHYPYVNIKQDSQTQLLASFRRSIASINPFSYRQVPSQDRAAFGLRWGNAWYAPNPYPNGIHF DRVFPTHYDPLAETNRTKANLQLIKYAPGNYSTLVVTSEKLPRPCIRTIQNYRRCQMVNGTEKCNSEAQDILAICPNWAL DHMKEKVRFYTKALAINNQTYIRAMQVEEYNQGRTVADVAPKTWIHGTRQHLRPDTMWADDRYTNITQTEINEAIKRVEA RKAREHEKKPVEQANVNANTGEQPVRVEKSLYP Q228N4 ATPTT6 Tetrahymena thermophila 0.029354383 2 LEVO MPVKEGQAKLWFSTKEEADAYDDKMISNIELKSQDYEDENFSPVFNRKTQEYFLEPSEKFKSDFAELLRPLRSLSFNQVV DRYVLIPPNHTFYRNWTYEKFLGGFGLSYLILRELPLRNFYARVFVMYAFAAKVLDHLGNPFPFSGHGQIVAAADRWNHW DVRCYDNVMKALKYIRIPTVQNNIPEATRWYGRQPGHLLRADTYWIPNLVSQRFAKHQPAHWDGTQNMPIFRLADPKHKD SYMVQFR I7MCQ6 ATPTT7 Tetrahymena thermophila 0.026355103999999997 2 LEVO MDNYFTAITLLGLRDQNLPPFKDARLQRYKSIKKMIDLIETTTKLAPPMPVELFMLNPTDPEWDDDMTYPTITHATALYK SSALAGNLFLYAYNYNNFTANIRLRTMRYLFPVVSLAIFGNIYWDYRSQLVKVNLFDEYIQARAQELVKQNEYLLEHEDV KRYVWWYEDLKETLARVHRQANNHKACDFKDSEIILQDFIRRYTNPKDNLPIKFHPQGQTF I7M980 ATPTT8 Tetrahymena thermophila 0.021782971 2 LEVO MEGFIQNKRKKEKEGEEEEESKEKRKQINQLNKQKQEEEKIYQQKKDQKRKKYLYQRKEMTIFAETWEASEYQYRNKANL KTLPVNHLGKLAELKFDFVEYKAHQLIACHLYERMTIHCMNQYGLFKDFYRPECLDAQYYFKTCVELNAAYGIQKKFFPE HFVGSPYARPVPQFQQLGL I7LVK6 ATPTT9 Tetrahymena thermophila 0.018199361 2 LEVO MKQKINKLLKNKGVQDKYKYLSKLILLDQEIKGKIKRKNKKEKQKRKNKLILEEMQNTTNIVHVPVHMGHTHYFDYIDSF PKLKEGPTLEENHITNQKILREQLISGQQGLEQNLCLRNCFKLSQKRYIEFCLDRKCGGADFQRAATILGYTKN Q24HK1 ATPTT10 Tetrahymena thermophila 0.017425703 2 LEVO MSNIFLELQDGDKTVYTHTSLIEESKQEQIQAIYDKVPQWTNGGRFLGFWLSMEAVNRVQSVAKLPIYYRAGIVATSTLL GGLVSSLVFWKSGNENQVAKLANGAPVYLKKWEVPELSKLYFFLDDDNNFKPSLNHHAVTQGRQYYKIYQHN I7LZE5 ATPTT11 Tetrahymena thermophila 0.017410811 2 LEVO MFRNILSLVTKPSKLSQKTFYNFAAAKNEVQVSKKQQQAGAKRDLTQYVEGQIVNRNQLTLKKQEDIEQYVLKLVRGYFR TTNKQGLNINSVLQDHGLDEFDSIELAMQVEEDLGYVISAETIPVLNKVKHFVNYINHVEQFKAENGKAPIA Q22DV8 ATPTT12 Tetrahymena thermophila 0.01734382 2 LEVO MSQDPKIVNPQLWPNPNKLRFADLYKYQGVEMKKINDSIKNYKAAKFYIGGILGGCLVFKFFIDAAVDKYIFGENGNGGK FLEMQTINSNYDYYYNRQFQRMRYLTEDPAGDDPLQKTKDEHLVDLGFIPKVFGANVEVRKRAPHDKYL I7M0G0 ATPTT13 Tetrahymena thermophila 0.016816249999999998 2 LEVO MNSLSSKKANSLVFKSIRNFTLQWGSLAERPMVDRVMSTSTWPVPYYQRLFKAYPIREKKDKMSLLLSDIDIDDTNWYQA KDFLRGSFRGRQIVDYVENNIASNTYILIQQDVANMAKAYVHDICGYIDVANKENVRILSKGDLI I7MLU7 ATPTT1 Tetrahymena thermophila 0.054917815999999994 2 LEVO MIHCLRNIRTVSALQSKISYNLGGGNKRKKTSGDLDNYDVLFVGANLGGICSNHFDKDTHGKYKCFVSFDQPINQIYSVR IPYEQQRVRKSEYIHFSKKSINQFTPSEMLAVKEILPEQNAVVLSSGRRIGYNQLVLATGLKHDFSQIKGFYEALEHPEH PVYANRDPETWRSAQHKYSKYISNFKSGDGYFCIPEYPYAGEVECFNFFVSDEVWKWAQHHGALSPKHTFTIVNANEKFV HYCDSADAFIKERLEKRGIRVEYNTKLLEVHQDGQKATFINTKTGEKSVRDYNNLYSIVPSKRQEFLDKAGLTNGNGLLN VDHQTLQHKKYKNIFGLGDAADLPTTKTFWAGWYQIAVVRNNVKRNLQGQTLNAHYDGFSKVPLFTGHQTLTYVAHSYGG VGNWQHLKHNNGGILAWMRYRSWAKGMAKKFQDFYNGARLGPPYHKVLKSFPELPGSPESQQSSGISKYFPTKTENKAAH I7LVQ8 Inhibitor of F1 (IF1) Tetrahymena thermophila 0.012987691 2 LEVO MNRSVNIAKNLIQTYRAMSVQSRFAFSTREEEWLDKRTKSQEKVYFDQEDRKAMKRLLEKLNTTSKFVEDSEYLAPQNLE VENILKRYHINYTQALIDELVDWKTGKN I7M7C0 ATPTT2 Tetrahymena thermophila 0.05434468 1 LEVO MKMEYLQSEEKKDAINKQIHKKEEKEEKEIKIKRKNKVKQRIQIINQIKKYIEAKQQKKQIQSKNQRKYKGRMINTRKQV FKCLWGAQPAYNFSRIINHLRGDPVYQDNTKDVSLRGTFLRGKYDDLPTMIFFTEACDLTANWIPFFTNPQYDILAHRNV WLLNPRNFGNSDRHPSFDLQEMSDDVMRFMYSQKISMATLGGHGIGGKIALAVGCYHAERVTGVFSIDSSPMDQRYHEAF KEFKGYVNALTEINFKTWSDKDVKVFLKENIKDPKWRSIFTNNISKNAKTQSDSFNFEINYLNHNLNFNKADSLGNWAVK NGIYTGRAHFIFPEYSRWVHLATNTLPMHKVCARVKGFGHDIFYVQGDENPLNHWVYDFENYANVVASKLNKFLHSYDGV HALLKDRTEIGNFMIPDRIKSRNDSKHIYGDYSPAHLHHNWRFNHIYEKHDELDKKLNEQ I7M7B9 CARDIOLIPIN 0.0014640429999999997 30 CDL 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE 0.0007901449999999999 6 PC1 PHOSPHATE ION 9.4971e-05 2 PO4 Ubiquinone-8 0.000727109 2 UQ8 ADENOSINE-5'-TRIPHOSPHATE 0.000507181 2 ATP MAGNESIUM ION 2.4305e-05 2 MG 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine 0.000744034 4 PEE NICOTINAMIDE-ADENINE-DINUCLEOTIDE 0.0006634249999999999 2 NAD singleParticle particle 0.75 7.5 Quantifoil R2/2 COPPER 300 ETHANE FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 165000.0 GIF Quantum LS 20 GATAN K2 QUANTUM (4k x 4k) COUNTING 30.9 1 CTFFIND 4.1.13 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 2.5 FSC 0.143 CUT-OFF RELION 3.1 beta 61157 MAXIMUM LIKELIHOOD RELION 3.1 beta MAXIMUM LIKELIHOOD RELION 3.1 beta emd_10859.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 498.0 498.0 498.0 90.0 90.0 90.0 X Y Z -0.055942725 0.1592571 0.00029939073 0.0032668915 0.83 0.83 0.83 0.018 AUTHOR ::::EMDATABANK.org::::EMD-10859:::: Local-resolution filtered full map of T. thermophila ATP synthase Fo-subcomplex emd_10859_msk_1.map emd_10859_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 498.0 498.0 498.0 90.0 90.0 90.0 X Y Z -0.051086564 0.08070301 0.00014494371 0.0056100627 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-10859:::: Half-map 1 emd_10859_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 498.0 498.0 498.0 90.0 90.0 90.0 X Y Z -0.04776569 0.081130974 0.00013275238 0.005625609 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-10859:::: Half-map 2