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Yorodumi- EMDB-34751: F1 domain of FoF1-ATPase from Bacillus PS3,101 degrees, highATP -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34751 | |||||||||||||||
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Title | F1 domain of FoF1-ATPase from Bacillus PS3,101 degrees, highATP | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | ATP synthase / MOTOR PROTEIN | |||||||||||||||
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. PS3 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Nakano A / Kishikawa J / Mitsuoka K / Yokoyama K | |||||||||||||||
Funding support | Japan, 4 items
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Citation | Journal: To Be Published Title: Rotation mechanism of ATP synthases driven by ATP hydrolysis Authors: Nakano A / Yokoyama K / Kishikawa J / Mitsuoka K | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34751.map.gz | 141.2 MB | EMDB map data format | |
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Header (meta data) | emd-34751-v30.xml emd-34751.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34751_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_34751.png | 75.7 KB | ||
Masks | emd_34751_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-34751.cif.gz | 6.6 KB | ||
Others | emd_34751_additional_1.map.gz emd_34751_half_map_1.map.gz emd_34751_half_map_2.map.gz | 165.6 MB 141.7 MB 141.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34751 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34751 | HTTPS FTP |
-Validation report
Summary document | emd_34751_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_34751_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_34751_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | emd_34751_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34751 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34751 | HTTPS FTP |
-Related structure data
Related structure data | 8hh4MC 8hh1C 8hh2C 8hh3C 8hh5C 8hh6C 8hh7C 8hh8C 8hh9C 8hhaC 8hhbC 8hhcC M: atomic model generated by this map C: citing same article (ref.) |
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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_34751.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_34751_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_34751_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34751_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34751_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : FoF1 from Bacillus PS3
Entire | Name: FoF1 from Bacillus PS3 |
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Components |
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-Supramolecule #1: FoF1 from Bacillus PS3
Supramolecule | Name: FoF1 from Bacillus PS3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Bacillus sp. PS3 (bacteria) |
Molecular weight | Theoretical: 530 KDa |
-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: 54.848598 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MSIRAEEISA LIKQQIENYE SQIQVSDVGT VIQVGDGIAR AHGLDNVMSG ELVEFANGVM GMALNLEENN VGIVILGPYT GIKEGDEVR RTGRIMEVPV GEALIGRVVN PLGQPVDGLG PVETTETRPI ESPAPGVMDR RSVHEPLQTG IKAIDALVPI G RGQRELII ...String: MSIRAEEISA LIKQQIENYE SQIQVSDVGT VIQVGDGIAR AHGLDNVMSG ELVEFANGVM GMALNLEENN VGIVILGPYT GIKEGDEVR RTGRIMEVPV GEALIGRVVN PLGQPVDGLG PVETTETRPI ESPAPGVMDR RSVHEPLQTG IKAIDALVPI G RGQRELII GDRQTGKTSV AIDTIINQKD QNMISIYVAI GQKESTVRTV VETLRKHGAL DYTIVVTASA SQPAPLLFLA PY AGVAMGE YFMYKGKHVL VVYDDLSKQA AAYRELSLLL RRPPGREAYP GDIFYLHSRL LERAAKLSDA KGGGSLTALP FVE TQAGDI SAYIPTNVIS ITDGQIFLQS DLFFSGVRPA INAGLSVSRV GGAAQIKAMK KVAGTLRLDL AAYRELEAFA QFGS DLDKA TQAKLARGAR TVEVLKQDLH QPIPVEKQVL IIYALTRGFL DDIPVEDVRR FEKEFYLFLD QNGQHLLEHI RTTKD LPNE DDLNKAIEAF KKTFVVSQ 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: 53.424625 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
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 VGERTREGND 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. PS3 (bacteria) |
Molecular weight | Theoretical: 31.859523 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAS PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL ...String: MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAS PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL YMYYNHYVSA IQQEVTERKL LPLTDLAENK QRTVYEFEPS QEEILDVLLP 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
Concentration | 5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5922 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.03843 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |