2021-02-24 REL PDBe PDBe PDBe 2020-07-21 2021-02-03 2021-02-03 2021-02-24 Medical Research Council (MRC, United Kingdom) MR/M009858/1 United Kingdom Medical Research Council (MRC, United Kingdom) MC_U105663150 United Kingdom Spikes TE Montgomery MG Walker JE Spikes TE Montgomery MG Walker JE Proc.Natl.Acad.Sci.USA US 118 2021 33542155 doi:10.1073/pnas.2021012118 1091-6490 0040 PNASA6 EMD-11001 other EM volume

ATP synthase state 1 monomer

EMD-11040 other EM volume

ATP synthase state 3 monomer

EMD-11428 other EM volume

ATP synthase dimer state1:state1

EMD-11429 other EM volume

ATP synthase dimer state1:state2

EMD-11430 associated EM volume Bovine ATP synthase Bovine ATP synthase 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

bovine ATP synthase inhibited by IF1 1-60His

0.007441 monomeric bovine ATP synthase 1 2 3 4 5 6 7 8 9 10 11 12 13 14 16 17

monomeric bovine ATP synthase inhibited by IF1 1-60His

Bos taurus Bovine ATP synthase 1 1 15 18 Bos taurus Escherichia coli ATP synthase alpha subunit Bos taurus

alpha-subunit residue 1 Residue GLN 1 of chains A, B, C is not an expression tag. Again the uniprot database is misleading. The DNA sequence for this protein encodes GLU. The actual residue is pyroGLU. However pyroGLU and pyroGLN are the same. Residue 481 in chains A, B, and C can be Gly or SER. e.g. in this structure should be GLY. We have seen SER in some of our previous structures of bovine F1-ATPase. We have used the following REMARK in other PDB files: REMARK 999 SEQUENCE REMARK 999 RESIDUE NUMBERING: BY CONVENTION, THE REMARK 999 FIFTH AMINO ACID (SERINE) IN THE BETA SUBUNITS (CHAINS D,E,F) IS REMARK 999 RESIDUE 1 AND THE FIRST FOUR AMINO ACIDS ARE NUMBERED -4 TO -1. REMARK 999 REFERENCE FOR THE ALPHA SUBUNIT J. E. WALKER, S. J. REMARK 999 POWELL,O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY,VOL 28,PP REMARK 999 4702-4708, 1989. REMARK 999 REMARK 999 SER 481 GLY IN CHAINS A, B AND C REMARK 999 WAS IDENTIFIED AS A GLY FROM THE PROTEIN REMARK 999 SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS REMARK 999 RESIDUE WAS AGC SER IN THREE CLONES WHILE IN TWO REMARK 999 OTHERS IT WAS GGC GLY. THE DIFFERENCE WAS THOUGHT TO REMARK 999 BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION REMARK 999 OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 REMARK 999 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN REMARK 999 THIS POSITION.

LEVO EKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLK GMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGP IGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAA PLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFY LHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKG IRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSR GVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALL SKIRTDGKISEESDAKLKEIVTNFLAGFEA ATP synthase beta subunit Bos taurus LEVO AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGES TVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAI HAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA HGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTG LTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERI TTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSR IMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQ PFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEE HS ATP synthase gamma subunit Bos taurus LEVO ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAE RELKPARVYGVGSLALYEKADIKTPEDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAAN LAAAGKEVKIIGVGDKIRSILHRTHSDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEF DEGSIIFNRFRSVISYKTEEKPIFSLDTISSAESMSIYDDIDADVLRNYQEYSLANIIYY SLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAALD ATP synthase delta subunit Bos taurus LEVO AEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAA HVPTLQVLRPGLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAVTL DMLDLGAAKANLEKAQSELLGAADEATRAEIQIRIEANEALVKALE ATP synthase epsilon subunit Bos taurus LEVO VAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE ATP synthase a subunit Bos taurus LEVO MNENLFTSFI TPVILGLPLV TLIVLFPSLL FPTSNRLVSN RFVTLQQWML QLVSKQMMSI HNSKGQTWTL MLMSLILFIG STNLLGLLPH SFTPTTQLSM NLGMAIPLWA GAVITGFRNK TKASLAHFLP QGTPTPLIPM LVIIETISLF IQPMALAVRL TANITAGHLL IHLIGGATLA LMSISTTTAL ITFTILILLT ILEFAVAMIQ AYVFTLLVSL YLHDNT ATP synthase b subunit Bos taurus LEVO PVPPLPEHGG KVRFGLIPEE FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITPETFSA ISTIGFLVYI VKKYGASVGE FADKLNEQKI AQLEEVKQAS IKQIQDAIDM EKSQQALVQK RHYLFDVQRN NIAMALEVTY RERLHRVYRE VKNRLDYHIS VQNMMRQKEQ EHMINWVEKR VVQSISAQQE KETIAKCIAD LKLLSKKAQA QPVM ATP synthase c subunit Bos taurus

Residue 43 is trimethylated. A post translational modification.

LEVO DIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSL(M3L)QQLFSYA ILGFALSEAMGLFCLMVAFLILFAM ATP synthase d subunit Bos taurus LEVO AGRKLALKTI DWVAFGEIIP RNQKAVANSL KSWNETLTSR LATLPEKPPA IDWAYYKANV AKAGLVDDFE KKFNALKVPI PEDKYTAQVD AEEKEDVKSC AEFLTQSKTR IQEYEKELEK MRNIIPFDQM TIEDLNEVFP ETKLDKKKYP YWPHRPIETL ATP synthase e subunit Bos taurus LEVO VPPVQVSPLI KLGRYSALFL GMAYGAKRYN YLKPRAEEER RLAAEEKKKR DEQKRIEREL AEAQEDTILK ATP synthase f subunit Bos taurus LEVO ASVVPLKEKKLLEVKLGELPSWILMRDFTPSGIAGAFQRGYYRYYNKYV NVKKGSIAGLSMVLAAYVFLNYCRSYKELKHERLRKYH ATP synthase g subunit Bos taurus LEVO AEFVRNLAEK APALVNAAVT YSKPRLATFW YYAKVELVPP TPAEIPTAIQ SLKKIINSAK TGSFKQLTVK EALLNGLVAT EVWMWFYVGE IIGKRGIIGY DV ATP synthase F6/h subunit Bos taurus LEVO NKELDPVQKL FVDKIREYRT KRQTSGGPVD AGPEYQQDLD RELFKLKQMY GKADMNTFPN FTFEDPKFEV VEKPQS ATP synthase j subunit (6.8PL) Bos taurus LEVO MLQSLIKKVW IPMKPYYTQA YQEIWVGTGL MAYIVYKIRS ADKRSKALKA SSAAPAHGHH ATP synthase k subunit (DAPIT) Bos taurus LEVO AGPEADAQF HFTGIKKYFN SYTLTGRMNC VLATYGSIAL IVLYFKLRSK KTPAVKAT ATP synthase OSCP subunit Bos taurus LEVO FAKLVRPPVQ IYGIEGRYAT ALYSAASKQN KLEQVEKELL RVGQILKEPK MAASLLNPYV KRSVKVKSLS DMTAKEKFSP LTSNLINLLA ENGRLTNTPA VISAFSTMMS VHRGEVPCTV TTASALDEAT LTELKTVLKS FLSKGQVLKL EVKIDPSIMG GMIVRIGEKY VDMSAKTKIQ KLSRAMREIL ATP synthase A6L/ATP8 subunit Bos taurus LEVO MPQLDTSTWL TMILSMFLTL FIIFQLKVSK HNFYHNPELT PTKMLKQNTP WETKWTKIYL PLLLPL ATP synthase inhibitor protein IF1 Bos taurus

Residues 1-60 of IF1 with a 6His tag

Escherichia coli LEVO GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHE NEISHHAKEIHHHHHH singleParticle particle 4.5 7.4 ETHANE 100 294 FEI VITROBOT MARK IV

The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting..

Nickel affinity purified filled by gel filtration

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 QUANTUM (4k x 4k) COUNTING 12.0 4.6 1 RELION 3.1 CTFFIND 4.1 2V7Q 9.0 FSC 0.143 CUT-OFF RELION 3.1 12721 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 2V7Q A 2V7Q B 2V7Q C 2V7Q D 2V7Q E 2V7Q F 2V7Q G 2V7Q H 2V7Q I 2V7Q J 2CLY A 2CLY B 2CLY C RIGID BODY FIT REAL emd_11430_msk_1.map emd_11430_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 524.0 524.0 524.0 90.0 90.0 90.0 X Y Z -0.093744926 0.0974782 0.00013758324 0.010381432 1.048 1.048 1.048 AUTHOR ::::EMDATABANK.org::::EMD-11430:::: ATP synthase dimer state1:state3 half map 1 emd_11430_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 524.0 524.0 524.0 90.0 90.0 90.0 X Y Z -0.08281928 0.09440618 0.00013107735 0.010496882 1.048 1.048 1.048 AUTHOR ::::EMDATABANK.org::::EMD-11430:::: ATP synthase dimer state1:state3 half map 2