+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40687 | |||||||||
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Title | PS3 F1 Rotorless, no ATP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | membrane / ATP synthase / electron transport / TRANSLOCASE | |||||||||
Function / homology | Function and homology information proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bacillus sp. PS3 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Sobti M / Stewart AG | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: Structure / Year: 2024 Title: The series of conformational states adopted by rotorless F-ATPase during its hydrolysis cycle. Authors: Meghna Sobti / Hiroshi Ueno / Simon H J Brown / Hiroyuki Noji / Alastair G Stewart / Abstract: FF ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalytic mechanism and isolated F-ATPase subcomplexes can also hydrolyze ATP to generate rotation of their ...FF ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalytic mechanism and isolated F-ATPase subcomplexes can also hydrolyze ATP to generate rotation of their central γ rotor subunit. As ATP is hydrolyzed, the F-ATPase cycles through a series of conformational states that mediates unidirectional rotation of the rotor. However, even in the absence of a rotor, the α and β subunits are still able to pass through a series of conformations, akin to those that generate rotation. Here, we use cryoelectron microscopy to establish the structures of these rotorless states. These structures indicate that cooperativity in this system is likely mediated by contacts between the β subunit lever domains, irrespective of the presence of the γ rotor subunit. These findings provide insight into how long-range information may be transferred in large biological systems. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40687.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-40687-v30.xml emd-40687.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_40687.png | 128.4 KB | ||
Filedesc metadata | emd-40687.cif.gz | 5.7 KB | ||
Others | emd_40687_additional_1.map.gz emd_40687_half_map_1.map.gz emd_40687_half_map_2.map.gz | 53.1 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40687 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40687 | HTTPS FTP |
-Validation report
Summary document | emd_40687_validation.pdf.gz | 937.2 KB | Display | EMDB validaton report |
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Full document | emd_40687_full_validation.pdf.gz | 936.8 KB | Display | |
Data in XML | emd_40687_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_40687_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40687 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40687 | HTTPS FTP |
-Related structure data
Related structure data | 8spvMC 8spwC 8spxC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40687.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_40687_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40687_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40687_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PS3 F1 Rotorless
Entire | Name: PS3 F1 Rotorless |
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Components |
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-Supramolecule #1: PS3 F1 Rotorless
Supramolecule | Name: PS3 F1 Rotorless / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus sp. PS3 (bacteria) |
-Macromolecule #1: ATP synthase subunit alpha
Macromolecule | Name: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase |
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Source (natural) | Organism: Bacillus sp. PS3 (bacteria) |
Molecular weight | Theoretical: 51.788184 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: DVGTVIQVGD GIARAHGLDN VMSGELVEFA NGVMGMALNL EENNVGIVIL GPYTGIKEGD EVRRTGRIME VPVGEALIGR VVNPLGQPV DGLGPVETTE TRPIESRAPG VMDRRSVHEP LQTGIKAIDA LVPIGRGQRE LIIGDRQTGK TSVAIDTIIN Q KDQNMISI ...String: DVGTVIQVGD GIARAHGLDN VMSGELVEFA NGVMGMALNL EENNVGIVIL GPYTGIKEGD EVRRTGRIME VPVGEALIGR VVNPLGQPV DGLGPVETTE TRPIESRAPG VMDRRSVHEP LQTGIKAIDA LVPIGRGQRE LIIGDRQTGK TSVAIDTIIN Q KDQNMISI YVAIGQKEST VRTVVETLRK HGALDYTIVV TASASQPAPL LFLAPYAGVA MGEYFMYKGK HVLVVYDDLS KQ AAAYREL SLLLRRPPGR EAYPGDIFYL HSRLLERAAK LSDAKGGGSL TALPFVETQA GDISAYIPTN VISITDGQIF LQS DLFFSG VRPAINAGLS VSRVGGAAQI KAMKKVAGTL RLDLAAYREL EAFAQFGSDL DKATQAKLAR GARTVEVLKQ DLHQ PIPVE KQVLIIYALT RGFLDDIPVE DVRRFEKEFY LFLDQNGQHL LEHIRTTKDL PNEDDLNKAI EAFKKTFVVS UniProtKB: ATP synthase subunit alpha |
-Macromolecule #2: ATP synthase subunit beta
Macromolecule | Name: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase |
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Source (natural) | Organism: Bacillus sp. PS3 (bacteria) |
Molecular weight | Theoretical: 51.584598 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI ...String: MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI QELIHNIAQE HGGISVFAGV GERTREGNDL YHEMKDSGVI SKTAMVFGQM NEPPGARMRV ALTGLTMAEY FR DEQGQDV LLFIDNIFRF TQAGSEVSAL LGRMPSAVGY QPTLATEMGQ LQERITSTAK GSITSIQAIY VPADDYTDPA PAT TFSHLD ATTNLERKLA EMGIYPAVDP LASTSRALAP EIVGEEHYQV ARKVQQTLQR YKELQDIIAI LGMDELSDED KLVV HRARR IQFFLSQNFH VAEQFTGQPG SYVPVKETVR GFKEILEGKY DHLPEDAFRL VGRIEEVVEK AKAMG UniProtKB: ATP synthase subunit beta |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 363810 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |