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Yorodumi- EMDB-6811: V/A-type ATPase/synthase from Thermus thermophilus, peripheral do... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6811 | |||||||||
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Title | V/A-type ATPase/synthase from Thermus thermophilus, peripheral domain, rotational state 1 | |||||||||
Map data | V/A-type ATPase/synthase from Thermus thermophilus, peripheral domain, state 1. | |||||||||
Sample |
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Function / homology | Function and homology information proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism ...proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / 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 | Thermus thermophilus HB8 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Nakanishi A / Kishikawa J / Tamakoshi M / Mitsuoka K / Yokoyama K | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Nat Commun / Year: 2018 Title: Cryo EM structure of intact rotary H-ATPase/synthase from Thermus thermophilus. Authors: Atsuko Nakanishi / Jun-Ichi Kishikawa / Masatada Tamakoshi / Kaoru Mitsuoka / Ken Yokoyama / Abstract: Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor ...Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor complex against the surrounding peripheral stator apparatus. Here, we present a large data set of single particle cryo-electron micrograph images of the V/A type H-rotary ATPase from the bacterium Thermus thermophilus, enabling the identification of three rotational states based on the orientation of the rotor subunit. Using masked refinement and classification with signal subtractions, we obtain homogeneous reconstructions for the whole complexes and soluble V domains. These reconstructions are of higher resolution than any EM map of intact rotary ATPase reported previously, providing a detailed molecular basis for how the rotary ATPase maintains structural integrity of the peripheral stator apparatus, and confirming the existence of a clear proton translocation path from both sides of the membrane. | |||||||||
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_6811.map.gz | 46.9 MB | EMDB map data format | |
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Header (meta data) | emd-6811-v30.xml emd-6811.xml | 20 KB 20 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6811_fsc.xml | 9.8 KB | Display | FSC data file |
Images | emd_6811.png | 55 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6811 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6811 | HTTPS FTP |
-Validation report
Summary document | emd_6811_validation.pdf.gz | 512.8 KB | Display | EMDB validaton report |
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Full document | emd_6811_full_validation.pdf.gz | 512.3 KB | Display | |
Data in XML | emd_6811_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_6811_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6811 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6811 | HTTPS FTP |
-Related structure data
Related structure data | 5y5yMC 6810C 6812C 6813C 5y5xC 5y5zC 5y60C M: atomic model generated by this map C: citing same article (ref.) |
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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_6811.map.gz / Format: CCP4 / Size: 50.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | V/A-type ATPase/synthase from Thermus thermophilus, peripheral domain, state 1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 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 : V/A-type ATPase/synthase from Thermus thermophilus, peripheral do...
Entire | Name: V/A-type ATPase/synthase from Thermus thermophilus, peripheral domai, rotational state 1. |
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Components |
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-Supramolecule #1: V/A-type ATPase/synthase from Thermus thermophilus, peripheral do...
Supramolecule | Name: V/A-type ATPase/synthase from Thermus thermophilus, peripheral domai, rotational state 1. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
Molecular weight | Theoretical: 650 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: Thermus thermophilus HB8 (bacteria) / Strain: HB8 |
Molecular weight | Theoretical: 63.69998 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 PFGSGKTVTQ 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 |
-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: Thermus thermophilus HB8 (bacteria) / Strain: HB8 |
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 |
-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: Thermus thermophilus HB8 (bacteria) / Strain: HB8 |
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 |
-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: Thermus thermophilus HB8 (bacteria) / Strain: HB8 |
Molecular weight | Theoretical: 11.294904 KDa |
Sequence | String: MAVIADPETA QGFRLAGLEG YGASSAEEAQ SLLETLVERG GYALVAVDEA LLPDPERAVE RLMRGRDLPV LLPIAGLKEA FQGHDVEGY MRELVRKTIG FDIKL |
-Macromolecule #5: V-type ATP synthase, subunit (VAPC-THERM)
Macromolecule | Name: V-type ATP synthase, subunit (VAPC-THERM) / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8 |
Molecular weight | Theoretical: 13.166218 KDa |
Sequence | String: MTGGLVLNAI SRAGGAMGGL GLIKSLAEKE KQLLERLEAA KKEAEERVKR AEAEAKALLE EAEAKAKALE AQYRERERAE TEALLARYR ERAEAEAKAV REKAMARLDE AVALVLKEVL P |
-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: Thermus thermophilus HB8 (bacteria) / Strain: HB8 |
Molecular weight | Theoretical: 20.699693 KDa |
Sequence | String: MSKLEAILSQ EVEAEIQALL QEAEAKAEAV KREAEEKAKA LLQARERALE AQYRAALRRA ESAGELLVAT ARTQARGEVL EEVRRRVRE ALEALPQKPE WPEVVRKLAL EALEALPGAK ALVANPEDLP HLEAMARERG VELQAEPALR LGVRAVGAEG K TQVENSLL ARMDRAWDAM SSKVAQALWG |
-Macromolecule #7: V-type ATP synthase subunit C
Macromolecule | Name: V-type ATP synthase subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8 |
Molecular weight | Theoretical: 35.96857 KDa |
Sequence | String: MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL ...String: MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL AKRFFEDVAK AAKGLDQPAL RDYLALEVDA ENLRTAFKLQ GSGLAPDAFF LKGGRFVDRV RFARLMEGDY AV LDELSGT PFSGLSGVRD LKALERGLRC VLLKEAKKGV QDPLGVGLVL AYVKEREWEA VRLRLLARRA YFGLPRAQVE EEV VCP |
-Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.027 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 26.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |