+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23115 | |||||||||
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Title | PS3 F1-ATPase Binding/TS Dwell | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ATPase / ATP synthase / TRANSLOCASE | |||||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / 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. (strain PS3) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Sobti M / Ueno H | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: The six steps of the complete F-ATPase rotary catalytic cycle. Authors: Meghna Sobti / Hiroshi Ueno / Hiroyuki Noji / Alastair G Stewart / Abstract: FF ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalysis mechanism. Isolated F-ATPase catalytic cores can hydrolyze ATP, passing through six intermediate ...FF ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalysis mechanism. Isolated F-ATPase catalytic cores can hydrolyze ATP, passing through six intermediate conformational states to generate rotation of their central γ-subunit. Although previous structural studies have contributed greatly to understanding rotary catalysis in the F-ATPase, the structure of an important conformational state (the binding-dwell) has remained elusive. Here, we exploit temperature and time-resolved cryo-electron microscopy to determine the structure of the binding- and catalytic-dwell states of Bacillus PS3 F-ATPase. Each state shows three catalytic β-subunits in different conformations, establishing the complete set of six states taken up during the catalytic cycle and providing molecular details for both the ATP binding and hydrolysis strokes. We also identify a potential phosphate-release tunnel that indicates how ADP and phosphate binding are coordinated during synthesis. Overall these findings provide a structural basis for the entire F-ATPase catalytic cycle. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23115.map.gz | 54.2 MB | EMDB map data format | |
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Header (meta data) | emd-23115-v30.xml emd-23115.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_23115.png | 70.3 KB | ||
Filedesc metadata | emd-23115.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23115 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23115 | HTTPS FTP |
-Validation report
Summary document | emd_23115_validation.pdf.gz | 427.4 KB | Display | EMDB validaton report |
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Full document | emd_23115_full_validation.pdf.gz | 427 KB | Display | |
Data in XML | emd_23115_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_23115_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23115 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23115 | HTTPS FTP |
-Related structure data
Related structure data | 7l1qMC 7l1rC 7l1sC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23115.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:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PS3 F1-ATPase Binding/TS Dwell
Entire | Name: PS3 F1-ATPase Binding/TS Dwell |
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Components |
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-Supramolecule #1: PS3 F1-ATPase Binding/TS Dwell
Supramolecule | Name: PS3 F1-ATPase Binding/TS Dwell / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Bacillus sp. (strain 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. (strain PS3) (bacteria) / Strain: PS3 |
Molecular weight | Theoretical: 55.881676 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSHHHHHHGS IRAEEISALI KQQIENYESQ IQVSDVGTVI QVGDGIARAH GLDNVMSGEL VEFANGVMGM ALNLEENNVG IVILGPYTG IKEGDEVRRT GRIMEVPVGE ALIGRVVNPL GQPVDGLGPV ETTETRPIES RAPGVMDRRS VHEPLQTGIK A IDALVPIG ...String: MSHHHHHHGS IRAEEISALI KQQIENYESQ IQVSDVGTVI QVGDGIARAH GLDNVMSGEL VEFANGVMGM ALNLEENNVG IVILGPYTG IKEGDEVRRT GRIMEVPVGE ALIGRVVNPL GQPVDGLGPV ETTETRPIES RAPGVMDRRS VHEPLQTGIK A IDALVPIG RGQRELIIGD RQTGKTSVAI DTIINQKDQN MISIYVAIGQ KESTVRTVVE TLRKHGALDY TIVVTASASQ PA PLLFLAP YAGVAMGEYF MYKGKHVLVV YDDLSKQAAA YRELSLLLRR PPGREAYPGD IFYLHSRLLE RAAKLSDAKG GGS LTALPF VETQAGDISA YIPTNVISIT DGQIFLQSDL FFSGVRPAIN AGLSVSRVGG AAQIKAMKKV AGTLRLDLAA YREL EAFAQ FGSDLDKATQ AKLARGARTV EVLKQDLHQP IPVEKQVLII YALTRGFLDD IPVEDVRRFE KEFYLFLDQN GQHLL EHIR TTKDLPNEDD LNKAIEAFKK TFVVSQ 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. (strain PS3) (bacteria) / Strain: PS3 |
Molecular weight | Theoretical: 53.410602 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHHHH HMTRGRVIQV MGPVVDVKFE NGHLPAIYNA LKIQHKARNE NEVDIDLTLE VALHLGDDTV RTIAMASTDG LIRGMEVID TGAPISVPVG EVTLGRVFNV LGEPIDLEGD IPADARRDPI HRPAPKFEEL ATEVEILETG IKVVDLLAPY I KGGKIGLF ...String: MHHHHHHHHH HMTRGRVIQV MGPVVDVKFE NGHLPAIYNA LKIQHKARNE NEVDIDLTLE VALHLGDDTV RTIAMASTDG LIRGMEVID TGAPISVPVG EVTLGRVFNV LGEPIDLEGD IPADARRDPI HRPAPKFEEL ATEVEILETG IKVVDLLAPY I KGGKIGLF GGAGVGKTVL IQELIHNIAQ EHGGISVFAG VGDRTREGND LYHEMKDSGV ISKTAMVFGQ MNEPPGARMR VA LTGLTMA EYFRDEQGQD VLLFIDNIFR FTQAGSEVSA LLGRMPSAVG YQPTLATEMG QLQERITSTA KGSITSIQAI YVP ADDYTD PAPATTFSHL DATTNLERKL AEMGIYPAVD PLASTSRALA PEIVGEEHYQ VARKVQQTLQ RYKELQDIIA ILGM DELSD EDKLVVHRAR RIQFFLSQNF HVAEQFTGQP GSYVPVKETV RGFKEILEGK YDHLPEDAFR LVGRIEEVVE KAKAM GVEV UniProtKB: ATP synthase subunit beta |
-Macromolecule #3: ATP synthase gamma chain
Macromolecule | Name: ATP synthase gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus sp. (strain PS3) (bacteria) / Strain: PS3 |
Molecular weight | Theoretical: 31.86557 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAC PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL ...String: MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAC PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL YMYYNHYVSA IQQEVTERKL LPLTDLAENK QRTVYEFEPS QEECLDVLLP QYAESLIYGA LLDAKASEHA AR MTAMKNA TDNANELIRT LTLSYNRARQ AAITQEITEI VAGANALQ UniProtKB: ATP synthase gamma chain |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #7: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 482550 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |