Structure of F-ATPase from Pichia angusta, state3

2024-05-15 REL PDBe PDBe PDBe 2016-10-04 2016-11-16 2016-11-16 2024-05-15 Structure of F-ATPase from Pichia angusta, state3 Vinothkumar KR Montgomery MG ATP synthase, hydrolase Vinothkumar KR Montgomery MG Liu S Walker JE Structure of the mitochondrial ATP synthase fromPichia angustadetermined by electron cryo-microscopy. Proc. Natl. Acad. Sci. U.S.A. US 113 12709 12714 2016 27791192 doi:10.1073/pnas.1615902113 1091-6490 0040 PNASA6 5lqx unknown Yeast F1FO ATP Synthase Yeast F1FO ATP Synthase 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

The complex comprises of the catalytic domain, membrane domain and peripheral stalk of the yeast ATP synthase.

Ogataea angusta A16 0.55 ATP synthase subunit f Ogataea angusta 0.0026562649999999997 1 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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) ATP synthase AAP1 subunit Ogataea angusta 0.002145636 1 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) ATP synthase subunit a Ogataea angusta 0.0014647969999999999

Helix 1 of subunit a

1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) ATP synthase subunit b Ogataea angusta 0.002315846

Helix 1 of subunit b

1 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)(UNK)(UNK) ATP synthase alpha subunit Ogataea angusta 0.055007535 3 LEVO ATAKAAPTEVSSILESKIRGVSDEANLDETGRVLSVGDGIARVFGLNNCQAEELVEFASGVKGMALNLEPGQVGIVLFGS DREVKEGEIVKRTGKIVDVPIGPGMLGRVVDALGNPIDGKGPIEATGYAIAQLKAPGILPRRSVFEPMQTGLKAVDALVP IGRGQRELIIGDRQTGKTAVALDTILNQKRWNDGNDESKKLYCVYVAVGQKRSTVAQLVQTLEQNDAMKYSIVVAATASE AAPLQYLAPFTACAIAEWFRDNGKHALIVYDDLSKQAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDANGG GSLTALPVIETQGGDVSAYIPTNVISITDGQIFLEAELFYKGIRPAINVGLSVSRVGSAAQVKAMKQVAGSLKLFLAQYR EVAAFAQFGSDLDASTKQTLSRGERLTQLLKQKQYSPQASEEQVPVIYAGVNGFLDNIPIERIPEFEEQFIAYLKANEGD ILEAIRTKGELSSELLDKLKSATETFVATF ATP synthase beta subunit Ogataea angusta 0.050852434 3 LEVO ATAGPASGKIRAVIGAVVDVQFEQGELPAILNALTIDQGNNQKLVLEVAQHLGENAVRAIAMDGTEGLVRGQTVVDTGAP ISVPVGRGTLGRIINVVGEPIDERGPIECKQRNPIHADPPSFVEQSTEAEVLETGIKVVDLLAPYARGGKIGLFGGAGVG KTVFIQELINNIAKAHGGFSVFTGVGERTREGNDLYREMKETGVINLEGESKVALVFGQMNEPPGARARVALTGLTIAEY FRDEEGQDVLLFVDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGLLQERITTTRKGSVTSVQAVYVPADDLTDPAP ATTFAHLDATTVLSRGISELGIYPAVDPLDSKSRLLDVSVVGQEHYDVATGVQQTLQAYKSLQDIIAILGMDELSEQDKL TVERARKIQRFLSQPFAVAEVFTGIEGKLVRLKDTIASFKAVLEGKYDHLPENAFYMVGGIEDVVAKAEKIAAEAN ATP synthase gamma subunit Ogataea angusta 0.029418238 1 LEVO ATLREIETRLKSIKNIEKITNTMKVVASTRMGRAQRAMASSRAFREGDSDFFATAETSTPETAEKTLIIAVSSDKGLCGS IHSQIAKATRAKLQETPNADVVTIGDKIKAQMLRTHSSNVVLSFNGVGKEAPTFWEASLIADEIRKLGDYDKIEVMYNKF VSGVAFEPSVFPSFSPISIEESPKLSEFELEEDQAIPTSLSQISLTNAILNAMAEGYASEISARRNAMDNASKNAGEMIN KYSILYNRTRQAVITNELVDIITGASSLD ATP synthase delta subunit Ogataea angusta 0.014171782999999999 1 LEVO AEAVNPDVLKVSLVAPHQAIFTNKEVSQVNLPASSGEMGVLANHVPTVEELAPGVVEVIESSGTASKYFVSGGFASILPG SKLSISTVEAHPLDAFSSENIKSLLAEAQKNASSADETVAAEAAIEIEVLEALQAAVH ATP synthase epsilon subunit Ogataea angusta 0.006910886 1 LEVO SSWQKAGISFNKYLAIAARTVQRSLKNDLKVAAEKRYISDAKVQKLEKGNVVSTTDLASNKSA ATP synthase inhibitor protein IF1 Bos taurus 0.0074620979999999995 1 Escherichia coli BL21(DE3) LEVO GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEIHHHHHH ATP synthase subunit c Ogataea angusta 0.00783738 10 LEVO MQLVLAAKYIGAAIATIGLTGAGIGIAIVFAALINGTSRNPSLRNTLFPFAILGFALSEATGLFCLMISFLLLYGV ATP synthase OSCP subunit Ogataea angusta 0.020678812 1 LEVO ASAAPIKPPVQLFGLDGTYATALFSASAKDSSIEKTFQSVQKLSSTISKDAKVAQVLSNPALSLNSRKEVVSVLSKELKL EPVVSNLLTVLAENNRLSLFDSIAKQFSVLNDAYNGVVEATVVSAKPLDSKILNRLTKSITNSKYVGPGKTLKIKNEVDP EILGGLIVEVADKSVDLSLASKVNKLNKVLSETI ATP synthase subunit b Ogataea angusta 0.022292331999999998 1 LEVO STPVDPKTKANALIDSLPGNSFLSKTGILATTAAASVYAISSELYVVNDESILLVTFLGFIALISKTVAPLYGEMAKNRT DHVVGLLNQARADHVNAVKTRIDQVSNLKDVVSTTKALFEMSKETAALEAEAFELKQKVAVASEAKSVLDSWVRYEAQVR QHEQEQLASTVISKVQSELQNAKFQDKVLAQAVEEVERLFAKEK ATP synthase subunit d Ogataea angusta 0.016427818 1 LEVO SSVAKSTANKLDWTKIVSKLGLSGQTAAALTSFKKRNDEAKRILFELKQQPSNVDFAFYKSTLKNTAIVDKIQSDVSKFT PSKANLSKQLNLIESFEAKALENAKETESVVLAELTDLEKTLENIES(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)(UNK)(UNK)(UNK) ATP synthase subunit h Ogataea angusta 0.001805216 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ATP synthase subunit a Ogataea angusta 0.027559775

Helices 4, 5 and 6 of subunit a

1 LEVO SPLDQFIINNLLEINSPFLNLSTLNFSTFSLYTLFVVLVISLTFILSIGGESNNLVKGSNWLIAIEAIFDTILNMVKGQI GGSVYGRYVPLVYTLFTFILVANLIGMVPYNFALSASLIYIIGISVSLWIGLTILGLFLNKAVFFSLFVPSGTPLPLVPV LVLIELLSYTARAISLGLRLAANTLSGHLLMSILGNLVKNLMSINYFTFIFGLIPLAGIFAIVILEFAIACIQAYVFAIL TSSYLKDSIYLH ATP synthase subunit a Ogataea angusta 0.0037626289999999995

Helices 2 and 3 of subunit a

1 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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) ADENOSINE-5'-TRIPHOSPHATE 0.000507181 1 ATP MAGNESIUM ION 2.4305e-05 5 MG ADENOSINE-5'-DIPHOSPHATE 0.000427201 5 ADP singleParticle particle 3.5 7.5 20.0 Tris-HCl 100.0 sodium chloride 2.0 Magnesium sulphate 1.0 ATP 0.05 Cymal-7 Quantifoil R0.6/1 GOLD 300 CARBON HOLEY GLOW DISCHARGE 75 AIR ETHANE 100 277.15 HOMEMADE PLUNGER

Grids were blotted for 12-14 seconds before plunging..

The enzyme with bound inhibitor protein extracted and purified in Cymal-7.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.8 5.0 47000.0 81395.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 87.5 FEI FALCON II (4k x 4k) INTEGRATING 4096 4096 1-32 4.0 64.0 1

The total exposure was 4 seconds resulting in 69 frames and a total dose of 64 e/A2. Frames were captured with an in-house protocol. For processing frames 1-32 were used.

123683

After 2D classification, the number of particles used for orientation determination and reconstruction was 100724 particles followed by per-particle motion correction and B-factor weighting.

EMD-2011 2 C1 7.9 FSC 0.143 CUT-OFF RELION 1.4 17590 NOT APPLICABLE NOT APPLICABLE 10 RELION 1.4

The whole data set were subjected to 3D classification to 10 classes with resolution limited to 12 A. Based on the position of the inhibitor protein, the classes were combined into three major groups. This map is called state 3, where the inhibitor protein is closest to the peripheral stalk.

emd_4100.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 525.0 525.0 525.0 90.0 90.0 90.0 X Y Z -0.16187143 0.51867765 0.00009730653 0.017747326 1.75 1.75 1.75 0.1 AUTHOR ::::EMDATABANK.org::::EMD-4100:::: RIGID BODY FIT

The refinement of whole data was done at 1.72 A sampling. The map was scaled to 1.75 A after comparison with the model.

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