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Yorodumi- EMDB-10469: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10469 | |||||||||
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Title | Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, peripheral stalk, rotational state 1 | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | mitochondria / ATP synthase / MEMBRANE PROTEIN | |||||||||
Biological species | Euglena gracilis (euglena) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Muhleip A / Amunts A | |||||||||
Citation | Journal: Elife / Year: 2019 Title: Structure of a mitochondrial ATP synthase with bound native cardiolipin. Authors: Alexander Mühleip / Sarah E McComas / Alexey Amunts / Abstract: The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum ...The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit . The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF) binds in a mode that is different from human, but conserved in Trypanosomatids. | |||||||||
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_10469.map.gz | 286.9 MB | EMDB map data format | |
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Header (meta data) | emd-10469-v30.xml emd-10469.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
Images | emd_10469.png | 56.5 KB | ||
Masks | emd_10469_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-10469.cif.gz | 6.5 KB | ||
Others | emd_10469_half_map_1.map.gz emd_10469_half_map_2.map.gz | 258.5 MB 258.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10469 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10469 | HTTPS FTP |
-Validation report
Summary document | emd_10469_validation.pdf.gz | 802.8 KB | Display | EMDB validaton report |
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Full document | emd_10469_full_validation.pdf.gz | 802.4 KB | Display | |
Data in XML | emd_10469_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | emd_10469_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10469 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10469 | HTTPS FTP |
-Related structure data
Related structure data | 6tdwMC 6tduC 6tdvC 6tdxC 6tdyC 6tdzC 6te0C 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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-Map
File | Download / File: emd_10469.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10469_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10469_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10469_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Euglena gracilis mitochondrial ATP synthase dimer, perpipheral st...
Entire | Name: Euglena gracilis mitochondrial ATP synthase dimer, perpipheral stalk region in rotational state 1 |
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Components |
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-Supramolecule #1: Euglena gracilis mitochondrial ATP synthase dimer, perpipheral st...
Supramolecule | Name: Euglena gracilis mitochondrial ATP synthase dimer, perpipheral stalk region in rotational state 1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 2 MDa |
-Macromolecule #1: ATPTB1
Macromolecule | Name: ATPTB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 56.010633 KDa |
Sequence | String: MTAVVKNLAK LPAATSQILT NVSKLQTFHG LLEERRDKYA PLAYHTYDNL KQKTTWHPIA HAWVDEGLPV SKKEYNEYCW LKKDMQRLL PLASPFVFGI YGILPLAVWL SNDGYLPSAF SSKKDIVSKK LEWYSSYGDD LRQQVGPMLQ HRLKRHLRGT L NNEHRLML ...String: MTAVVKNLAK LPAATSQILT NVSKLQTFHG LLEERRDKYA PLAYHTYDNL KQKTTWHPIA HAWVDEGLPV SKKEYNEYCW LKKDMQRLL PLASPFVFGI YGILPLAVWL SNDGYLPSAF SSKKDIVSKK LEWYSSYGDD LRQQVGPMLQ HRLKRHLRGT L NNEHRLML DEVTESYKEI FYSHYTGQLR DVRKCAHLRL YDGTSTVLLL TNKEPVELTS ELLQKWNAIK AAKLSPEEEK KA RNEALIE AYKEQELHGG PHVKHMQGYG IPSDTPLLGE NAKGDQYTQP PESASIPLEQ LEWTGDTVFI PAEYRTEVED WGR ELTKLA NQFLLLPWRF VSNAWNQRRL VSWFEEILQE DALIAKEGGV QALSDDELKV ALLDRAVIRC DEELTRGDME ARYK EISWL MSLRNPFIVL AWQTGYYRST YSPEDDLPEA SILPKLNRTV LDVDVHNELA PDHPEKPLPR VHPALYPNSH LALAK EVAV LAK |
-Macromolecule #2: subunit d
Macromolecule | Name: subunit d / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 53.928289 KDa |
Sequence | String: MMRRACRIIR PSHVRGVSGV APTIYLRSKA ALPATSTTDV RPQLYALQRF AKAQLKTATE AERAAIEADI ARYQEYLDSD LEKLKQDVA EDTAKKQKLI PLLDRYPDVP IEKIPEHANV LLKKIDACLE ILSKDIGEVT DAEAHEMYFE TSKFQILHIY T GCVASFPE ...String: MMRRACRIIR PSHVRGVSGV APTIYLRSKA ALPATSTTDV RPQLYALQRF AKAQLKTATE AERAAIEADI ARYQEYLDSD LEKLKQDVA EDTAKKQKLI PLLDRYPDVP IEKIPEHANV LLKKIDACLE ILSKDIGEVT DAEAHEMYFE TSKFQILHIY T GCVASFPE GDVPPGAVEC LPGQVIRTKV NGEDVMLEID EVDPGYQVCW FKPDVPLPEN AEILWSYPYE PTAALPTGTT WE EGQANVL IPAEPTPEAA VWPPTPVTNV YAPMAEKLAL KSNPELKVLF KEALLQPAKL LPLDVDYQCS HDREVVEAKR DRY LTALVE AEQAPPLPFT PDVLQLQLEH NVLKGELIDR LRALEYTIVT EQLQARLHER RLRGDVIDEW EELDYHPLVR DDTY LAIDF GDPTFGRYIW KLFPHTDGDE ECMFKDTRLD VLPPQVNPLN AILAQHTAQT PVHRSLEKRL WTEVRATAVS E |
-Macromolecule #3: ATPTB3
Macromolecule | Name: ATPTB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 35.175836 KDa |
Sequence | String: MAAKTIPFVA STALGERLFA GVQKVLAAAK APVSLVQTDA KFAPADAKYL LAEPLSAAAT GELANKYGLS SKVTSGAASQ FYPNSIYPS LNVEVVQNLY ALSNPAFSSL SATTTKAVTV KDESAIKLAE LQKETERNIS SFFRDEANKS VQATLRLACD K AIKTKADK ...String: MAAKTIPFVA STALGERLFA GVQKVLAAAK APVSLVQTDA KFAPADAKYL LAEPLSAAAT GELANKYGLS SKVTSGAASQ FYPNSIYPS LNVEVVQNLY ALSNPAFSSL SATTTKAVTV KDESAIKLAE LQKETERNIS SFFRDEANKS VQATLRLACD K AIKTKADK KTVMVVTKPH GDAFDDLLAQ VTKSESDGRA DELRNSSVSV EPTLVGNAWP KLVMFPEGVN VVVCGPNASG DQ VAQLFVG IAGGTGMVAQ QLVGDAVVFT SANAEDNENP TGALLAASNL LTALGHEAEA KKIAAAVAKA YTTDRILPKE LPG GKADLE AFIDAVAKHA SA |
-Macromolecule #4: ATPTB4
Macromolecule | Name: ATPTB4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 18.83351 KDa |
Sequence | String: MFRGFRPVLA ADAVKFQTLY NVLTGKQHLK DQVPVKDCNL TAIFGASWKA DLNKWFDSEY APKLPAAERD SAKKSLDLYL KRVDLTRYT REELTTYGIL ACGPGKVDAL TEKHLLETGK ARLEELTAGL GNKDEGVNAF RKEVEQEGKY ANWPAEKSKA L ADKVIAAS P |
-Macromolecule #5: oligomycin sensitivity conferrring protein (OSCP)
Macromolecule | Name: oligomycin sensitivity conferrring protein (OSCP) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 29.56452 KDa |
Sequence | String: MHMRRAVSVF GRCRSLNGLR NYAVPSPKYI EIYQSDFSRN AYPLELLGGS HVDFAKLLYS FADQVENKKF EVYVEDFKKL DSIIAEKGP FWAEEKIFQS PTFQGLSEGF KFILGWIQSE GAIDRLENVR LAYKELVNEA RKETTATVIV AKEPSGNDLA E IRKQVEEL ...String: MHMRRAVSVF GRCRSLNGLR NYAVPSPKYI EIYQSDFSRN AYPLELLGGS HVDFAKLLYS FADQVENKKF EVYVEDFKKL DSIIAEKGP FWAEEKIFQS PTFQGLSEGF KFILGWIQSE GAIDRLENVR LAYKELVNEA RKETTATVIV AKEPSGNDLA E IRKQVEEL HKESPLKDYK LVLETKVDPS IGGGYILEVC NQVVNRSAAA AAAETAALAK ASAAQVDWTS LPAAPPRPSP SA PDTLIRL LGSVVDDLAD ADKVEQKYGA |
-Macromolecule #6: subunit b
Macromolecule | Name: subunit b / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 12.673109 KDa |
Sequence | String: MPSTSPADKD VPMSILHTHG LSYVNWCMSL APGLLVFEGF FRARYYRSRV PPSRTVLMNG LKMRMFSLAR QQAPKIVHKP VLSPIPEHL RLVKNVAQVQ IDMLKLLNAQ AAK |
-Macromolecule #7: subunit 8
Macromolecule | Name: subunit 8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 7.112312 KDa |
Sequence | String: LIPVSLVDLI NINIIFYILL LYTLLLFFIP LFLASINYTY HYIYKYYNYN YNFINNNT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blot. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 9045 / Average exposure time: 10.0 sec. / Average electron dose: 36.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |