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 2020-06-26 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 rotor domain, state 3 Spikes T Montgomery MG ATP synthase, mitochondria, mammalian, complex, SYNTHASE, 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 EMD-11039 other EM volume EMD-11040 other EM volume EMD-11149 other EM volume EMD-11195 other EM volume EMD-11196 other EM volume 6zik FULLOVERLAP Imaged sample bovine dimeric ATP synthase (1.2 MDa) Imaged sample bovine dimeric ATP synthase (1.2 MDa) 0 1 2 3 4
A focussed map of the rotor domain was created and the model fitted and refined to that. The rotor domain (chains GHIKLMNOPQR) has a mass of 0.112 MDa.
Bos taurus 1.2 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 ATP synthase F(0) complex subunit C2, mitochondrial Bos taurus 0.0076530339999999995
Residue 43 is tri-methyl lysine. A post translational modifcation.
8 LEVO DIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSL(M3L)QQLFSYAILGFALSEAMGLFCLMVAFLILFAM P07926 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
The starting models were 2V7Q and 2XND docked into the map using COOT or CHIMERA.
 C2 3.66 FSC 0.143 CUT-OFF RELION 3.1 61485 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_11227.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 -0.08851765 0.14220707 -0.00006499437 0.0018199327 1.048 1.048 1.048 0.03 AUTHOR State 3 rotor main map 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_11227_msk_1.map emd_11227_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 -0.02243539 0.053505298 -0.00006554651 0.0011867075 1.048 1.048 1.048 AUTHOR State 3 rotor half map 1 emd_11227_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 -0.022383433 0.05420098 -0.000064442225 0.0011846412 1.048 1.048 1.048 AUTHOR State 3 rotor half map 2