2024-05-22 REL PDBe PDBe PDBe 2020-05-04 2020-09-09 2020-09-09 2024-05-22 Medical Research Council (MRC, United Kingdom) MR/M009858/1 United Kingdom Medical Research Council (MRC, United Kingdom) MC_U105663150 United Kingdom bovine ATP synthase F1-peripheral stalk domain, state 1 Spikes T Montgomery MG ATP synthase, mitochondria, mammalian, complex, HYDROLASE Spikes TE Montgomery MG Walker JE Structure of the dimeric ATP synthase from bovine mitochondria. Proc.Natl.Acad.Sci.USA US 117 23519 23526 2020 32900941 doi:10.1073/pnas.2013998117 1091-6490 0040 PNASA6 6yy0 FULLOVERLAP Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His 0 1 2 3 4 5 6 7 8 9 10 0.007441 ATP synthase F1 domain 1 1 2 3 4 5
The F1 domain of ATP synthase
Bos taurus ATP synthase peripheral stalk 1 7 8 9 10
Part of the stator of the enzyme
Bos taurus ATPase inhibitor, mitochondrial 1 6
ATPase inhibitor truncated version of IF1 with residues 1-60 and HIS6 tag
Bos taurus ATP synthase subunit alpha, mitochondrial Bos taurus 0.055302190999999994
In chains ABC, Glu 1 is technically correct. 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. There is no density to support a SER. It should be considered microheterogeneity. We have used the following REMARK in previous PDB files: 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.
3 LEVO EKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDK LIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIG RGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAA PLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGGGS LTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREV AAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALL GKIRTDGKISEESDAKLKEIVTNFLAGFEA P19483 ATP synthase subunit beta, mitochondrial Bos taurus 0.051757836
The mature protein starts AAQA. UNIPROT are updating entry P00829 to reflect this.
3 LEVO AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVL DSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFG GAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTG LTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVPADD LTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDEL SEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEE HS P00829 7.1.2.2 ATP synthase subunit gamma, mitochondrial Bos taurus 0.030300759999999996 1 LEVO ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTPEDKKKHLIIGVSSDRGLCGA IHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTHSDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSI IFNRFRSVISYKTEEKPIFSLDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS EMIDKLTLTFNRTRQAVITKELIEIISGAAALD P05631 ATP synthase subunit delta, mitochondrial Bos taurus 0.015074813 1 LEVO AEAAAAQAPAAGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSKYFVSSG SVTVNADSSVQLLAEEAVTLDMLDLGAAKANLEKAQSELLGAADEATRAEIQIRIEANEALVKALE P05630 ATP synthase subunit epsilon, mitochondrial Bos taurus 0.005662693 1 LEVO VAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKKE P05632 ATPase inhibitor, mitochondrial Bos taurus 0.0074620979999999995
bovine ATP synthase inhibitor protein IF1 residues 1-60 plus 6 Histidines
1 Escherichia coli LEVO GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEIHHHHHH P01096 ATP synthase subunit O, mitochondrial Bos taurus 0.020959777 1 LEVO FAKLVRPPVQIYGIEGRYATALYSAASKQNKLEQVEKELLRVGQILKEPKMAASLLNPYVKRSVKVKSLSDMTAKEKFSP LTSNLINLLAENGRLTNTPAVISAFSTMMSVHRGEVPCTVTTASALDEATLTELKTVLKSFLSKGQVLKLEVKIDPSIMG GMIVRIGEKYVDMSAKTKIQKLSRAMREIL P13621 ATP synthase F(0) complex subunit B1, mitochondrial Bos taurus 0.024702708999999996 1 LEVO PVPPLPEHGGKVRFGLIPEEFFQFLYPKTGVTGPYVLGTGLILYLLSKEIYVITPETFSAISTIGFLVYIVKKYGASVGE FADKLNEQKIAQLEEVKQASIKQIQDAIDMEKSQQALVQKRHYLFDVQRNNIAMALEVTYRERLHRVYREVKNRLDYHIS VQNMMRQKEQEHMINWVEKRVVQSISAQQEKETIAKCIADLKLLSKKAQAQPVM P13619 ATP synthase subunit d, mitochondrial Bos taurus 0.018588256 1 LEVO AGRKLALKTIDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKANVAKAGLVDDFEKKFNALKVPI PEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKELEKMRNIIPFDQMTIEDLNEVFPETKLDKKKYPYWPHRPIETL P13620 ATP synthase-coupling factor 6, mitochondrial Bos taurus 0.008971079 1 LEVO NKELDPVQKLFVDKIREYRTKRQTSGGPVDAGPEYQQDLDRELFKLKQMYGKADMNTFPNFTFEDPKFEVVEKPQS P02721 ADENOSINE-5'-TRIPHOSPHATE 0.000507181 3 ATP MAGNESIUM ION 2.4305e-05 5 MG ADENOSINE-5'-DIPHOSPHATE 0.000427201 3 ADP water 1.8015e-05 17 HOH singleParticle particle 4.5 7.4 UltrAuFoil GOLD GLOW DISCHARGE OTHER
Post glow discharging the grids were PEgylated with 5 mM mercaptopoly(ethyleneglycol)carboxylic acid (PEG-thiol).
 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 2V7Q C2 3.23 FSC 0.143 CUT-OFF RELION 3.1 101165 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_11001.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 -0.078340724 0.15106414 -0.0000018713765 0.003140522 1.048 1.048 1.048 0.0271 AUTHOR State1 F1 focussed half map 1 2V7Q A PDB experimental model 2V7Q B PDB experimental model 2V7Q C PDB experimental model 2V7Q D PDB experimental model 2V7Q E PDB experimental model 2V7Q F PDB experimental model 2V7Q G PDB experimental model 2V7Q H PDB experimental model 2V7Q I PDB experimental model 2V7Q J PDB experimental model 2CLY A PDB experimental model 2CLY B PDB experimental model 2CLY C PDB experimental model RIGID BODY FIT REAL emd_11001_msk_1.map emd_11001_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 -0.038467452 0.09916817 -0.0000029195419 0.0035915172 1.048 1.048 1.048 AUTHOR State1 F1 focussed half map 2 emd_11001_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 -0.037950885 0.09183199 -0.0000008232113 0.0035791763 1.048 1.048 1.048 AUTHOR State1 F1 focussed mask