2020-09-30 REL PDBe PDBe PDBe 2019-04-12 2019-07-03 2019-07-03 2020-09-30 Max Planck Society Germany European Molecular Biology Organization ALTF 702 2016 Germany Murphy BJ Klusch N Yildiz O Kuhlbrandt W Murphy BJ Klusch N Langer J Mills DJ Yildiz O Kuhlbrandt W Science US 364 2019 31221832 doi:10.1126/science.aaw9128 1095-9203 0038 SCIEAS EMD-4821 associated EM volume

Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, composite map

6rdk FULLOVERLAP Mitochondrial F-ATP synthase dimer from Polytomella sp. Pringsheim 198.80 Mitochondrial F-ATP synthase dimer from Polytomella sp. Pringsheim 198.80 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Polytomella sp. Pringsheim 198.80 1.6 ASA-10: Polytomella F-ATP synthase associated subunit 10 Polytomella sp. Pringsheim 198.80 0.008731866 1 LEVO MSYSAYFAKAGFQFPAGLSALVAGIVALNVCTGRPTKGTKEISNAEYNATPIGYLQSPDQHPTAFPKVPGMKDVHGSPHH HH ATP synthase associated protein ASA1 Polytomella sp. Pringsheim 198.80 0.068679906 1 LEVO MMRAAQKAKQELPATVLTQTRSYLAPLRSDFTEEITAPKVASASNLVNEWNNKKQATENLMKLLQAYKDIGDAKSEPLLK NHNPRTFEDRDYPVPDFRTQNLKAGDVPKFFDTVISTRASAAIASKDKFWAGRKTEAEAASAKASAAFPRVAVPEWKKGK TVSIENLNTVTDKYAAALVPKRKLALPVLPEGVKKAVEDFAASVGQAKNASEVSELLAKSLAEKAVVTEGGKVVEGFSYV SKAVAAKVIATRRAEVHERLLKLWAKRLLVSPELAIVPLNEFDAQLASKFEGISPKYQELLSAVAQGNKTFAQRLNSSPA FSSFLLKREKAESEVPPSELELEAAQKAAELEDPEVALRTLLGPQMEALGASDLLLSEQIRVITEHRYTPDRLQYKEGMK LADKIAAQEAALKEELKVIYGDNVDVKHFQASPRTPVQQLFDSLKNAAANKERAAKEAAAAASPYLAYAVTKKQEVQADP SNIPFDEVLYPQLSEELLELELSDIREDEIALEKAEEEELWLLTLTQQFKHIQKHFGIDLPHSVVAHMDPLLIKKIDWET TNALEDFDITLDDMGAEDAKEQWGAENLSHHFLPLIRYRRDLARKNGDRYGPDLVNGN Mitochondrial ATP synthase subunit ASA2 Polytomella sp. Pringsheim 198.80 0.044842121 1 LEVO ENDVPAILKEIDSLVSREAVSAKEVSDAAVALTYLQVKANRRLWGKVLEKAGAAQDYDAASLTNLLWAINTGGVEHFKTV AELAGPAVSLLPSLSPVQLSIVVEALGGAGVKNYELYNKASAVVVSKIGEFKPAEIARVLYGVAFGGVNDVALAKAAGKV FASTEVDSRTAAQALYALAKLGRADKATVDALLKSFKKGTESASDAAAASFALGSLSFKAEKAIVDALKASAGDLAPAQA VEAAYGLALSGATDAEAFKALFGVVAPAIEKAPDALEVSSLAQLHVASTISGAKLPAAVGSFVAKAFGLAADAARLKRSS AESALVADVAAATAVAFGAQYRPEVASAVASYVKTAPDGSVLDIAITKGDAKVLVQAVPSSLLTSTTPAKPLGHVAAYSK VREAQGYAVAVVPANEFEALPDQKAKAQYVLAAIKKVAPSF Mitochondrial F1F0 ATP synthase associated 32 kDa protein Polytomella sp. Pringsheim 198.80 0.034850363 1 LEVO MRQASRLALSIRQAGNVEAASAVPAMTRQFSAPGSHEHHETPLSKVMPTVVSIPRKVACLALGATKKVVCGLASSGPSQN LVSTFANKVIVEENLVNVAEIDVPFWSYWLSSAGFTSKDAFVKFAEAVKPKVAALSTSDITNLTVAFKRANYYDKDLFTG IEANVSANFTKFETEQLLQIVATFDAFNHSSVAFLDDVADSITYCNHYLAPVRAGADELATLLTYYAKNGHERADLLATV ARGFSEVSLGKLSAAQRKDTVLSALKAFQTFGFYPESIEAVIGAALVSPAEYSAEELKEVEAVKVAAENALGGEFVLIQE GAHGH Mitochondrial ATP synthase associated protein ASA4 Polytomella sp. Pringsheim 198.80 0.031275113 1 LEVO ATEPAVSKKEVLYFLSSKDAESSTAVKSYLKSLYAGAQVEATETDASELIAQLEKKYLSAQVVEPGVHNIALPLGESGSA PVKRYAAELFNLGAQAGFECPFIEVSKKFGQETATSETVKDVLNKTKSYVSADYNAALNEVLSSVEAEINGPVLFDGKTE GFKKFAAKAKAVAVSRGLPADTILAYCAGSANEDAADKVSKEFFTWFESAYTADAAAEVKAIEAEAASILDRHLAKPVAQ IRKEQASAYASLLKRAETAKGAKWAEKYLEDVKAVQWFDASVAEAPASGPKVAA Mitochondrial F1F0 ATP synthase associated 14 kDa protein Polytomella sp. Pringsheim 198.80 0.014004376 1 LEVO MKLLPESLQQEAATAAVVASWVLWHLDTQLLPTIMREHKLHACWAAAAKRYNEKLFKLNPSYDRVLSLPAVSKNQVLENV FHTAPKAPVEHLEKMVSANSKVYDALNLQSKRVLIWQVKPALF Mitochondrial ATP synthase subunit ASA6 Polytomella sp. Pringsheim 198.80 0.01590429 1 LEVO MMLRTLTRSSAVAGQAVRLFKTSAAAAEGNSVAGIIKSVNETSGANLLSSLKTIKAQAAPIYPAAASSTGYSTQAKIALF GALSWILYRADGQSKAHEWIVDLNLNVLQAAWLISFSSLIPFRAVYFAFRGMAPATASTLNGLKTFSSISL Mitochondrial ATP synthase associated protein ASA7 Polytomella sp. Pringsheim 198.80 0.02055316 1 LEVO MSSVRAGVEAGRRDLTTFTFSGLQDAPVAALSGSIKLNVAAKAGKAEVTVAAGAAKAATQVSAAALRKLSGSKISLAEVA RISVLHSSIQNYLLSLSNERYQLLSQWPDFTTMYGKDFYYRAHPEDLKKFYDAADEYYKLYETVTEFDSLSALASQVVPN YAARRRSTVHPAIGSTVADGAFTNFLLSKQ Mitochondrial ATP synthase subunit ASA8 Polytomella sp. Pringsheim 198.80 0.009883389 1 LEVO MVLGEVYLKDILRTPPTGAIPANVPHPFQTSFYTYATKKLIPRHWYLLGGFTFTITLYGILDGLRDSGKKKAYDEAIHAG KTPYTAGGH Mitochondrial ATP synthase subunit ASA9 Polytomella sp. Pringsheim 198.80 0.011001712 1 LEVO MAVTSFLGKAFEKYFYDFSAYEQFGLNRFLSSKGQYVALRHVGFVMVGVNVLLAANFPFNPPFPTIGMCPAGWEGTWVCQ ADKAKALEMYKEWKKSN Mitochondrial ATP synthase subunit c Polytomella sp. Pringsheim 198.80 0.012664013 10 LEVO MSVQRLSLGAARCLSAGVARVQASQALVAQKAVAVAPTRAQAAPAEVAQVRSMSVLAASKMVGAGCATIALAGVGAGLGV MFGSLINGAARNPNIAKQLVGYALLGFALTESIALFSLLVVFLILFA Mitochondrial ATP synthase subunit 6 Polytomella sp. Pringsheim 198.80 0.034802344 1 LEVO MSVLSSVSMGSRIGSSLLGRSSAYLAQCGFSTRSNLNGSIDTSSSVFQALSSDNENKPAASPLNVKLPGMSCSSILLPKT SRIAVPFGNQTMAMSSVRDVKTGSLPTNFLTGVYRFWRSQNPAEKPHDPVNDRLLPAVVDASDKRASIGTWATTFFCTII SCNLLGLMPFNEAPTSGLGFATGLGVSVWATATILGLSKTGFKFPGHFIPGGTPWPMAFIFVPLETISYTFRAVSLGVRL WVNMLAGHTLLHILTGMALALPFSLGFFSMVPATFGVCCLLSALVGLEYLVAVLQSGVFSILSTVYVGEFNHDKFIGPAA KIVKKIH Mitochondrial ATP synthase subunit OSCP Polytomella sp. Pringsheim 198.80 0.025530793 1 LEVO MLARVASVALRRAEGKIMPQMVRALSVSAASAAQAELKLPTAPLQLSGTSAQIATLLWQVAAKENQLDKVQDELYQFIEL FKQHSELRRLATDPFVPTLVRTKIISSVLKDSGASEITKKLFEALADEGALSALLEVTVNYEELMLAHKKEVYCTVITAE PLDKLERVELTKKAEKFVDAGFKLVMQEKIDKKLLGGFVIEFSDRRVDMSTAKKVEEFNNFVNKLVLSI epsilon: Polytomella F-ATP synthase epsilon subunit Polytomella sp. Pringsheim 198.80 0.008205479 1 LEVO MCAPSGPFYRVAGMSYLRYSNICADLLRNVLKEPFKAKAQARQAIHFRQAPYVDGKAGASKVYELENGIPKTAN Mitochondrial ATP synthase subunit delta Polytomella sp. Pringsheim 198.80 0.020880533 1 LEVO MFGLKRAVTVGRRFISTSAARMEAAAPAGPKEFTEVWNKKAPSTLIVPEFPSNYTAVKAVGEGQVHGDAFPVNFYTPHSI LSQAQKDTVVLPGVDGYFGVKASHVPTIAQLKPGVVELHSGAESEKFFVSGGFAFVHPNGVTDICVLEAATLDQVDPAAV KSALAAASAAQPTDEFEQAANRAAIELYSALESAVEAKA ATP synthase gamma chain, mitochondrial Polytomella sp. Pringsheim 198.80 0.034639594 1 LEVO MALRKAVLSLGLSQGVAAEAVLGSGMFNAVQHESVRYASNQAVKQRIRAIKNIGKITKAMKMVAASKMKNAQIAVEQSRG LVDPFVRLFGDFPAVNSNKSVVVAVTSDKGLCGGLNSNITKYTRATLATTESEGKDVVVVSIGDKGRSQLTRIESQRYQL AIADTYKVRVTFGQASLIVEELIKHNPQSYQILFNKFRSAISFKPTVATILSPDLLEKQLEDVTGNSLDAYDIEASHERS DVLRDLTEFHLGVTLYNAMLENNCSEHASRMSAMENSTKSAGEMLGKLTLDYNRKRQATITTELIEIIAGASALMDE ATP synthase subunit alpha Polytomella sp. Pringsheim 198.80 0.060766152 3 LEVO MRSPAAFVARSGLFKASLGQSNWAQKAEQMMASVTRTFAADAKALDELRKPKFSSKYLIQHVSQKLIPAVKEWEKSYQPP VIHLGRVLSVGDGIARVYGLKSVQAGELVCFDSGVKGMALNLQADHVGVVVFGNDSVIHQGDLVYRTGQIVNVPIGPGTL GRVTDGLGQPIDGKGPLTNVRSSLVEVKAPGIIARQSVREPLFTGVKAVDALVPIGRGQRELIIGDRQTGKTAVAIDAII HQKNCNEQVPKAQRVYCVYVAVGQKRSTVAQLVKLFTQTGAMRYTIMVSATASDAAPLQFLAPYSGCAMAEYFRDTGKHG LIIYDDLSKQSVAYRQMSLLLRRPPGREAFPGDVFYLHSRLLERAAKLSKELGGGSLTAFPVIETQAGDVSAYIATNVIS ITDGQIFLETELFYKGIRPALNVGLSVSRVGSAAQFPGMKQVAGTLKLELAQYREVAAFAQFGSDLDAATQYVLERGARL TEMLKQKQFAPIPIERQTVAVYAATKGFLDKVRVQDIVAAEEAVISQVNPAVFKILKANGKITPALDAHLKAELRKVKLP GA ATP synthase subunit beta Polytomella sp. Pringsheim 198.80 0.06193907 3 LEVO MALRYAAGLAKNVVQRQGASLNIARAFAAEPAPAIDAGYVSQVIGPVVDVRFDGELPSILSSLEVEGHSVRLVLEVAQHM GDNTVRCIAMDSTDGLVRGQKVVDTGSPIKVPVGRGTLGRIMNVIGEPVDEQGPIDAADIWSIHREAPEFTEQSTEQEIL VTGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELINNVAKAHGGFSVFAGVGERTREGNDLYREMIESGVIKLGAERG NSKCTLVYGQMNEPPGARARVALTGLTVAEYFRDIEGQDVLLFVDNIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGG LQERITTTTKGSITSVQAVYVPADDLTDPAPATTFAHLDATTVLSRSIAELGIYPAVDPLDSTSRMLNPNVIGAEHYNVA RGVQKVLQDYKNLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGTPGKYVDLADTISGFQGVLTGKYDD LPEMAFYMVGDIKEVKEKADKMAKDIASRKEADNKKVSEELKDIPSLDKLVSEIKEVVIEEDDGLEEDFKAEALSSETVV LNEEGKSVPLPKKN 7.1.2.2 ZINC ION 6.5409e-05 1 ZN ADENOSINE-5'-TRIPHOSPHATE 0.000507181 3 ATP MAGNESIUM ION 2.4305e-05 5 MG ADENOSINE-5'-DIPHOSPHATE 0.000427201 2 ADP singleParticle particle 3.5 7.8 C-flat-2/1 COPPER 400 GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 -0.4 -5.0 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 3840 3712 35.0 1 735197 CTFFIND 4.1.10 C1 3.7 FSC 0.143 CUT-OFF RELION 3 72402 NOT APPLICABLE NOT APPLICABLE RELION 3 REAL