2025-04-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION database_2 em_3d_fitting_list em_admin pdbx_initial_refinement_model _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBe PDBe 2020-05-14 2020-09-09 2020-09-09 2025-04-09 Medical Research Council (MRC, United Kingdom) MR/M009858/1 United Kingdom Medical Research Council (MRC, United Kingdom) MC_U105663150 United Kingdom bovine ATP synthase F1c8-peripheral stalk domain, state 3 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 EMD-11001 other EM volume
ATP synthase, state 1
 EMD-11039 other EM volume
ATP synthase, state 2
 6z1u 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)
Bos taurus ATP synthase subunit alpha, mitochondrial Bos taurus 0.055302190999999994
Chain ABC res 481: Residue 481 in chains A, B, and C in this structure should be GLY. There is no density to support a SER and negative density appears if you try SER. 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 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.
3 LEVO EKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDK LIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIG RGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAA PLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGGGS LTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREV AAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALL GKIRTDGKISEESDAKLKEIVTNFLAGFEA P19483 ATP synthase subunit beta, mitochondrial Bos taurus 0.051757836 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
ATP synthase inhibitor protein IF1 residues 1-60 with a 6HIS affinity tag
1 Escherichia coli LEVO GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEIHHHHHH P01096 ATP synthase F(0) complex subunit C2, mitochondrial Bos taurus 0.0076530339999999995
Trimethyl-lysine at position 43
8 LEVO DIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSL(M3L)QQLFSYAILGFALSEAMGLFCLMVAFLILFAM P07926 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-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 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 3.47 FSC 0.143 CUT-OFF RELION 3.1 61458 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_11040.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 -0.07156458 0.11974778 -0.0000032163075 0.00284674 1.048 1.048 1.048 0.0267 AUTHOR State 3 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 2XND M PDB experimental model RIGID BODY FIT REAL emd_11040_msk_1.map emd_11040_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 -0.046302285 0.09374995 -0.0000035419403 0.0042460295 1.048 1.048 1.048 AUTHOR State 3 half map 2 emd_11040_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 -0.043296535 0.08655381 -0.0000028906748 0.004255508 1.048 1.048 1.048 AUTHOR State 3 half map 1