2025-03-12 REL PDBj INITIAL_RELEASE REPOSITORY PDBj PDBj 2024-07-08 2025-03-12 2025-03-12 2025-03-12 Japan Society for the Promotion of Science (JSPS) JP17H01544 Japan Japan Science and Technology JPMJCR19S5 Japan Japan Agency for Medical Research and Development (AMED) JP22am121003 Japan Other government Toyonaga T Kato T Kawamoto A Miyata T Kawakami K Fujita J Hamaguchi T Namba K Miyata M ATPase, Complex, kinase, Ring, HYDROLASE Toyonaga T Kato T Kawamoto A Miyata T Kawakami K Fujita J Hamaguchi T Namba K Miyata M Sci Adv US 11 eadr9319 eadr9319 2025 40009674 doi:10.1126/sciadv.adr9319 2375-2548 9io5 FULLOVERLAP G1-ATPase dimer from Mycoplasma mobile gliding machinery G1-ATPase dimer from Mycoplasma mobile gliding machinery 0 1 2 3 4 5 6 7 8 Mycoplasma mobile 163K P476R gli521 G1-ATPase subunit beta Mycoplasma mobile 163K P476R gli521 0.088510383 6 LEVO MTTNNLTELEILNIKKYLKTVNLNTLRAYARRNVKDFSEKLIKVKVIEKIVEHDKKFDNIEDSIFVQISSQFGVNFETIL DGSFFLGQKAAKAMPKTFDTKIISETKSVQKFEEVKFATSSKTEKIISEEKEILHLIEQSKRDRDFIDNFSKILEEKNLT EEHQHMSCQVCYDHEKKHSDHNEKYATEHCDACVYHDFSDLDPEFVASTYTEEEIIHNLLFKLYSVEQLALFTIDQLNAL LFARGLGLEKNKVRAIKSLLTLQTSYEFMEKSQAALLPKVSFNPTNPLKPIEEKEFTIFGEIVEIRSQVYKIRIDKAEEE VLPKVIFYADVNGKEIQLEVADIFDKNLVSTFVLGNETGLKIGTKVKSKNQSYAIKISKRLLGRVIDPIGKILDDSIATP VHGNMYAPLEMQHDSEATRYVVSPKNAILETGIKVIDVLLPIPKGGKTGLLGGAGVGKTVIVQELINAFIKFHDGVSVFA GIGERIREGHELWKEAEALGFLNKTAFIFGQMNESPGLRFRSGISGVKVAEYFRNNLGKSVLLFMDNIFRYVQAGSEISS LLEKTPSAVGYQPTLFSEMGQLQERINSTKDGDITSIQAMYIPADDFTDPAAVAAFAHFDSTIILSRQLAAEGVYPAIDP LESNSKMLSIKYTSREHLDIAKKTVQTLEKTKTLEDIINILGFDALSEDDKKVVEVGRRLKWFLTQPFVVAEKFSGVPGK FVRLKDSLKGIKTILDGDLNHIPVSYFSFVGVVEEIIEKFNLDAKKEALKNELEQNQKDLASII Q6KIC3 3.6.3.14 G1-ATPase subunit alpha Mycoplasma mobile 163K P476R gli521 0.058794667999999994 6 LEVO MKNLKITAIKDNLIFVEGEHQFSFLEIIKFSDKVEGVVLKANDRSAIVAILNEDKDLNLTVGSLAEATGELYKIPIYDNY LGSIINVLGESLVKQYERTNVALDKKYVFTEAQPIFTRSAVNEPLVTGITVVDGVLPVGRGQKELIIGDRGTGKTAIALN AMLAQENTDVINIFIAIGKKRDEIVEIYGTFKKHNILHKSIIVSAASDDAVAARYLAPYAGMAIAEFFQQIGKDVLVVMD DLTNHADAYRELSLLAGIAPAREAYPGDIFYVHSSLLERGGKYGPEFGGGSITILPIAQTLAGDISGYIPTNLISITDGQ IYTSAKLFNEGTRPAIDVNLSVSRLGSAAQSKFMAFASSGLKKIYTEYKYLKRLSSFSSKISNRDLETLQKGKAFESLID QAEYEVIDYETSAILFLLLKKGFLNFYTEKTEALKVIIGVIKVFLAKDVLGRKMRAILVEHGIDSIVWNLYLNHMILPLL KYHLLSELQYLATNREFIKKFKDIRNDGRILLAYERKGYERGIAYDYK Q6KIC4 3.6.3.14 G1-ATPase subunit gamma Mycoplasma mobile 163K P476R gli521 0.039810602 2 LEVO MKRKDVEEKKQNLDFYHNYIDISKIKVLQKLNEEIASLNMLKLQKGESHYLLNRIINKWFPHNSNIYHELHHENDRKELY ILIDPKKLDLFSEALLRKLSQTVKERIRPDKDFVITVGTNVDNIARQLNLNIIDHYDLDLFNQIDDFANRIGELVDVGLN NKIFNYVSLLIAQSSTKNNGGLVQERIVPFNTKNIKVWNESNQDENGMPIVSEENEVEIMSYAKTLRNINFKKHTWLPNI NTFYEQFVKSVFKQELFEFKSISVIEELKIELQLLDEKKKRLEEQKKELILKWNRARKEEATLQSTLLFSAFKVKNQKST RDEILRLSKGKNRNGA Q6KIC7 Phosphoglycerate kinase Mycoplasma mobile 163K P476R gli521 0.056680749999999995 3 LEVO MKKTLDQISLKNKKVIIRVDFNVPIVNGIVTSNKRIEAVIPTIKKVVNEGGKAILMSHLGRVKSEEDLKKKSLAPVVEIL VNLLGMPITFVPATNGTELEETINSMKSGEIVMMENTRFEDLNNDAESSNNPDLGMYWASLGDVFINDAFGTVHRKHASN VGISTYIAESGIGYLVEKEIKNLDKALSRPERPIVAILGGAKVSDKIGVLNNLLKYVDKIIIGGAMAYTFLAAQGIGIGK SLVEEDKIDLAREYLKNNLDKFVLPIDYALAKDFEDVKPFYNLENTLEIPNGYMGLDIGPKSIEVFKKYIKDAKTILWNG PLGVTEFKYFKEGTKAIAKAITELKGNVYTVVGGGDSVAIIEELGLDRRFSHVSTGGGATLEFLEGKELPGIQAIQNEGE LGRTKEEIFSILTQNSEEVLHEHTAAFSTSEVEPANEEFPSEYNDSNSQTYFSNEVENDEDFLLNTNDFPTREASFPNEV KTEEIILNENDDEFDIEDEELDSLPNDDIKF Q6KHJ1 2.7.2.3 G1-ATPase subunit D Mycoplasma mobile 163K P476R gli521 0.033753953 6 LEVO MKKTDKNQTGKEIMKKELLIKTNEQDINLAPKSQSTSKKLSNTWNYEELINQTKEIDVNSKIVKTELEYVEEDSRLRKEK IELIQKNYDNLNAKPLVGVDLYESYSLVLNKSAWNYNEIIQRDTQLTILDMALQVHLFLYEGKIIDIAHIQKIIKTFVLN VFAKIIKGVPIVLNPIIIFDSVRFDKSKILPVAVANPKLMPPLGVQDWDTIVDEDEEIKKIVSTFIKLLENALTVGHEVE FFQDTLLVRNVDGITSLYVSEKAAQVFNNSVIDQIMPEKPKYEALEDPFSNKK Q6KIC8 G1-ATPase subunit E Mycoplasma mobile 163K P476R gli521 0.013264168 1 LEVO MTKNIFANKIANQKAYFKRDIKTVHTFLGRVNYIQRASKFNDEKRVFRPLQIELSGTNEIVDIYLEATTYISKKALDEIR QNSYIFLEAKWLPESNFLNNPLFEIQNIVIEN Q6KHS6 UNKNOWN HELIX Mycoplasma mobile 163K P476R gli521 0.0011243779999999999 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) UNKNOWN HELIX Mycoplasma mobile 163K P476R gli521 0.000783958 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) ADENOSINE-5'-TRIPHOSPHATE 0.000507181 8 ATP MAGNESIUM ION 2.4305e-05 10 MG ADENOSINE-5'-DIPHOSPHATE 0.000427201 2 ADP PHOSPHATE ION 9.4971e-05 2 PO4 singleParticle particle 1 7.3 8.1 Na2HPO4 disodium hydrogenphosphate 1.5 KH2PO4 potassium dihydrogen phosphate 2.7 KCl potassium chloride 137.0 NaCl sodium chloride 1.0 MgCl2 magnesium chloride 0.1 C32H58N2O7S CHAPS Quantifoil R1.2/1.3 GOLD 200 GRAPHENE GLOW DISCHARGE 20

Epoxidized graphene grid (EG-grid) was used.

ETHANE 100 277 FEI VITROBOT MARK IV JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 1.8 60000.0 JEOL CRYOSPECPORTER NITROGEN In-column Omega Filter 20 GATAN K3 (6k x 4k) 1 7350 3.3 80.0 1 633820

ab initio

C1 FOURIER SPACE 3.2 FSC 0.143 CUT-OFF cryoSPARC 3.3.2 RELION 4.0 Mask creation and post-processing were done in RELION 4.0. 142490 MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 3 cryoSPARC 3.3.2 emd_60718_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 528 528 528 0 0 0 528 528 528 459.36002 459.36002 459.36002 90.0 90.0 90.0 X Y Z -1.1910428 3.0188391 0.003322835 0.051298477 0.87 0.87 0.87 AUTHOR ::::EMDATABANK.org::::EMD-60718:::: emd_60718_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 528 528 528 0 0 0 528 528 528 459.36002 459.36002 459.36002 90.0 90.0 90.0 X Y Z -1.0727915 2.8491914 0.003418524 0.05039513 0.87 0.87 0.87 AUTHOR ::::EMDATABANK.org::::EMD-60718:::: emd_60718_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 528 528 528 0 0 0 528 528 528 459.36002 459.36002 459.36002 90.0 90.0 90.0 X Y Z -2.2845595 3.0034359 0.0013204708 0.24996023 0.87 0.87 0.87 AUTHOR ::::EMDATABANK.org::::EMD-60718:::: emd_60718_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 528 528 528 0 0 0 528 528 528 459.36002 459.36002 459.36002 90.0 90.0 90.0 X Y Z -2.1273403 3.1444378 0.0013536965 0.24981917 0.87 0.87 0.87 AUTHOR ::::EMDATABANK.org::::EMD-60718::::