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Open data
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Basic information
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Title | V1EG of V/A-ATPase from Thermus thermophilus, state1-1 | |||||||||||||||||||||
![]() | V1EG of V/A-ATPase from Thermus thremophilus, state1-1 | |||||||||||||||||||||
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![]() | rotary ATPase / V-type ATPase / ATP synthase / Thermus thermophilus / chemo-mechanical coupling / MOTOR PROTEIN | |||||||||||||||||||||
Function / homology | ![]() proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / plant-type vacuole / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism ...proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / plant-type vacuole / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lysosomal membrane / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||||||||
![]() | Kishikawa J / Nakanishi A / Nakano A / Saeki S / Furuta A / Kato T / Mitsuoka K / Yokoyama K | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases. Authors: J Kishikawa / A Nakanishi / A Nakano / S Saeki / A Furuta / T Kato / K Mistuoka / K Yokoyama / ![]() Abstract: V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FF ATP synthase. When powered by ATP hydrolysis, the V domain rotates the central rotor against the AB hexamer, ...V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FF ATP synthase. When powered by ATP hydrolysis, the V domain rotates the central rotor against the AB hexamer, composed of three catalytic AB dimers adopting different conformations (AB, AB, and AB). Here, we report the atomic models of 18 catalytic intermediates of the V domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not rotate immediately after binding of ATP to the V. Instead, three events proceed simultaneously with the 120˚ rotation of the shaft: hydrolysis of ATP in AB, zipper movement in AB by the binding ATP, and unzipper movement in AB with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in AB, rather than the power stroke model proposed previously for F-ATPase. | |||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 326 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.6 KB 23.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.9 KB | Display | ![]() |
Images | ![]() | 112 KB | ||
Masks | ![]() | 347.6 MB | ![]() | |
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() | 14.2 MB 14.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vaiMC ![]() 7vajC ![]() 7vakC ![]() 7valC ![]() 7vamC ![]() 7vanC ![]() 7vaoC ![]() 7vapC ![]() 7vaqC ![]() 7varC ![]() 7vasC ![]() 7vatC ![]() 7vauC ![]() 7vavC ![]() 7vawC ![]() 7vaxC ![]() 7vayC ![]() 7vb0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | V1EG of V/A-ATPase from Thermus thremophilus, state1-1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: V1EG of V/A-ATPase from Thermus thremophilus, state1-1, halfmapA
File | emd_31842_half_map_1.map | ||||||||||||
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Annotation | V1EG of V/A-ATPase from Thermus thremophilus, state1-1, halfmapA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: V1EG of V/A-ATPase from Thermus thremophilus, state1-1, halfmapB
File | emd_31842_half_map_2.map | ||||||||||||
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Annotation | V1EG of V/A-ATPase from Thermus thremophilus, state1-1, halfmapB | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Nucleotide-free V/A-ATPase from Thermus thermophilus, state1
Entire | Name: Nucleotide-free V/A-ATPase from Thermus thermophilus, state1 |
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Components |
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-Supramolecule #1: Nucleotide-free V/A-ATPase from Thermus thermophilus, state1
Supramolecule | Name: Nucleotide-free V/A-ATPase from Thermus thermophilus, state1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 700 KDa |
-Macromolecule #1: V-type ATP synthase alpha chain
Macromolecule | Name: V-type ATP synthase alpha chain / 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: ![]() ![]() |
Molecular weight | Theoretical: 63.669957 KDa |
Sequence | String: MIQGVIQKIA GPAVIAKGML GARMYDICKV GEEGLVGEII RLDGDTAFVQ VYEDTSGLKV GEPVVSTGLP LAVELGPGML NGIYDGIQR PLERIREKTG IYITRGVVVH ALDREKKWAW TPMVKPGDEV RGGMVLGTVP EFGFTHKILV PPDVRGRVKE V KPAGEYTV ...String: MIQGVIQKIA GPAVIAKGML GARMYDICKV GEEGLVGEII RLDGDTAFVQ VYEDTSGLKV GEPVVSTGLP LAVELGPGML NGIYDGIQR PLERIREKTG IYITRGVVVH ALDREKKWAW TPMVKPGDEV RGGMVLGTVP EFGFTHKILV PPDVRGRVKE V KPAGEYTV EEPVVVLEDG TELKMYHTWP VRRARPVQRK LDPNTPFLTG MRILDVLFPV AMGGTAAIPG PFGAGKSVTQ QS LAKWSNA DVVVYVGCGE RGNEMTDVLV EFPELTDPKT GGPLMHRTVL IANTSNMPVA AREASIYVGV TIAEYFRDQG FSV ALMADS TSRWAEALRE ISSRLEEMPA EEGYPPYLAA RLAAFYERAG KVITLGGEEG AVTIVGAVSP PGGDMSEPVT QSTL RIVGA FWRLDASLAF RRHFPAINWN GSYSLFTSAL DPWYRENVAE DYPELRDAIS ELLQREAGLQ EIVQLVGPDA LQDAE RLVI EVGRIIREDF LQQNAYHEVD AYCSMKKAYG IMKMILAFYK EAEAAIKRGV SIDEILQLPV LERIGRARYV SEEEFP AYF EEAMKEIQGA FKALA UniProtKB: V-type ATP synthase alpha chain |
-Macromolecule #2: V-type ATP synthase beta chain
Macromolecule | Name: V-type ATP synthase beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 53.2195 KDa |
Sequence | String: MDLLKKEYTG ITYISGPLLF VENAKDLAYG AIVDIKDGTG RVRGGQVIEV SEEYAVIQVF EETTGLDLAT TSVSLVEDVA RLGVSKEML GRRFNGIGKP IDGLPPITPE KRLPITGLPL NPVARRKPEQ FIQTGISTID VMNTLVRGQK LPIFSGSGLP A NEIAAQIA ...String: MDLLKKEYTG ITYISGPLLF VENAKDLAYG AIVDIKDGTG RVRGGQVIEV SEEYAVIQVF EETTGLDLAT TSVSLVEDVA RLGVSKEML GRRFNGIGKP IDGLPPITPE KRLPITGLPL NPVARRKPEQ FIQTGISTID VMNTLVRGQK LPIFSGSGLP A NEIAAQIA RQATVRPDLS GEGEKEEPFA VVFAAMGITQ RELSYFIQEF ERTGALSRSV LFLNKADDPT IERILTPRMA LT VAEYLAF EHDYHVLVIL TDMTNYCEAL REIGAAREEI PGRRGYPGYM YTDLATIYER AGVVEGKKGS VTQIPILSMP DDD RTHPIP DLTGYITEGQ IQLSRELHRK GIYPPIDPLP SLSRLMNNGV GKGKTREDHK QVSDQLYSAY ANGVDIRKLV AIIG EDALT ENDRRYLQFA DAFERFFINQ GQQNRSIEES LQIAWALLSM LPQGELKRIS KDHIGKYYGQ KLEEIWGAPQ ALD UniProtKB: V-type ATP synthase beta chain |
-Macromolecule #3: V-type ATP synthase subunit D
Macromolecule | Name: V-type ATP synthase subunit D / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.715566 KDa |
Sequence | String: MSQVSPTRMN LLQRRGQLRL AQKGVDLLKK KRDALVAEFF GLVREAMEAR KALDQAAKEA YAALLLAQAF DGPEVVAGAA LGVPPLEGV EAEVENVWGS KVPRLKATFP DGALLSPVGT PAYTLEASRA FRRYAEALIR VANTETRLKK IGEEIKKTTR R VNALEQVV ...String: MSQVSPTRMN LLQRRGQLRL AQKGVDLLKK KRDALVAEFF GLVREAMEAR KALDQAAKEA YAALLLAQAF DGPEVVAGAA LGVPPLEGV EAEVENVWGS KVPRLKATFP DGALLSPVGT PAYTLEASRA FRRYAEALIR VANTETRLKK IGEEIKKTTR R VNALEQVV IPGIRAQIRF IQQVLEQRER EDTFRLKRIK GKIEAREAEE EGGRPNPQVE IGAGL UniProtKB: V-type ATP synthase subunit D |
-Macromolecule #4: V-type ATP synthase subunit F
Macromolecule | Name: V-type ATP synthase subunit F / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.294904 KDa |
Sequence | String: MAVIADPETA QGFRLAGLEG YGASSAEEAQ SLLETLVERG GYALVAVDEA LLPDPERAVE RLMRGRDLPV LLPIAGLKEA FQGHDVEGY MRELVRKTIG FDIKL UniProtKB: V-type ATP synthase subunit F |
-Macromolecule #5: V-type ATP synthase subunit G
Macromolecule | Name: V-type ATP synthase subunit G / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.166218 KDa |
Sequence | String: MTGGLVLNAI SRAGGAMGGL GLIKSLAEKE KQLLERLEAA KKEAEERVKR AEAEAKALLE EAEAKAKALE AQYRERERAE TEALLARYR ERAEAEAKAV REKAMARLDE AVALVLKEVL P UniProtKB: V-type ATP synthase, subunit (VAPC-THERM) |
-Macromolecule #6: V-type ATP synthase subunit E
Macromolecule | Name: V-type ATP synthase subunit E / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.645582 KDa |
Sequence | String: MSKLEAILSQ EVEAEIQALL QEAEAKAEAV KREAEEKAKA LLQARERALE AQYRAALRRA ESAGELLVAT ARTQARGEVL EEVRRRVRE ALEALPQKPE WPEVVRKLAL EALEALPGAK ALVANPEDLP HLEALARERG VELQAEPALR LGVRAVGAEG K TQVENSLL ARLDRAWDAL SSKVAQALWG UniProtKB: V-type ATP synthase subunit E |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 5.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.045 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |