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- EMDB-15562: rotor of the Trypanosoma brucei mitochondrial ATP synthase dimer -
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Open data
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Basic information
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Title | rotor of the Trypanosoma brucei mitochondrial ATP synthase dimer | |||||||||
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![]() | ATP synthase / mitochondria / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() H+-transporting two-sector ATPase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / : / : / : / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity ...H+-transporting two-sector ATPase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / : / : / : / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / mitochondrion Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Muehleip A / Gahura O / Zikova A / Amunts A | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() Title: An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases. Authors: Ondřej Gahura / Alexander Mühleip / Carolina Hierro-Yap / Brian Panicucci / Minal Jain / David Hollaus / Martina Slapničková / Alena Zíková / Alexey Amunts / ![]() ![]() Abstract: Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM ...Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 543.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.1 KB 18.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.8 KB | Display | ![]() |
Images | ![]() | 53.8 KB | ||
Masks | ![]() | 669.9 MB | ![]() | |
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 537.6 MB 537.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 892.6 KB | Display | ![]() |
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Full document | ![]() | 892.1 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ap9MC ![]() 8ap6C ![]() 8ap7C ![]() 8ap8C ![]() 8apaC ![]() 8apbC ![]() 8apcC ![]() 8apdC ![]() 8apeC ![]() 8apfC ![]() 8apgC ![]() 8aphC ![]() 8apjC ![]() 8apkC 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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
-Entire : mitochondrial ATP synthase dimer from Trypanosoma brucei
Entire | Name: mitochondrial ATP synthase dimer from Trypanosoma brucei |
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Components |
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-Supramolecule #1: mitochondrial ATP synthase dimer from Trypanosoma brucei
Supramolecule | Name: mitochondrial ATP synthase dimer from Trypanosoma brucei type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: ATP synthase gamma subunit
Macromolecule | Name: ATP synthase gamma subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34.472254 KDa |
Sequence | String: MSGKLRLYKE KLEGYNRFYS IVKTIKMVTL AKYRAAQGRI RTRDFSLRYT ELAFSKPQAS RDAVVAAKNA LVYIPITTNR GSCGALNSN IVRCIDSVVS SKMVLMPVGK RGIDSFSKLY PDEFRYGIIN DMKESMHFGY ATFVIENAYE VSKDADRYQV I FNRFVSAG ...String: MSGKLRLYKE KLEGYNRFYS IVKTIKMVTL AKYRAAQGRI RTRDFSLRYT ELAFSKPQAS RDAVVAAKNA LVYIPITTNR GSCGALNSN IVRCIDSVVS SKMVLMPVGK RGIDSFSKLY PDEFRYGIIN DMKESMHFGY ATFVIENAYE VSKDADRYQV I FNRFVSAG VQRNAVYNIP SYEKWKEDLA DAASSDNQKN RYLFANALQN EEEQLIRDFF DFHAALAVLN AVGENELSEQ AA RLVAVEG QLTNISSLQQ RTSSLYNKTR QFGITAALIE ILSAMSSLEG NAMKGVRRNK FWEGAVTK UniProtKB: ATP synthase subunit gamma, mitochondrial |
-Macromolecule #2: ATP synthase, epsilon chain, putative
Macromolecule | Name: ATP synthase, epsilon chain, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.172938 KDa |
Sequence | String: MFRTFGRRLV SCTLPLLQSA PHDLPEGFEF MEHKVVNKDI HAPHENLETL RLTLTRQDEF LLREEPVKCV TVTGTNGEYG IYPGHAYKI VQLNPSPLTV EYTDGTTKKY FVSGGFAHIN NEGSCDVNTV ECTLLDDLDL AIAEKELAAQ QAALGSAKDD K AKSVVEIR ISVIEAVIAA LKHH UniProtKB: ATP synthase, epsilon chain, putative |
-Macromolecule #3: ATP synthase subunit epsilon, mitochondrial
Macromolecule | Name: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 8.70689 KDa |
Sequence | String: MIRRSCALLS SSWRDHGISY LKYLNVCTET LHSTVKESRR AKYERWSKPC YTAQRPDGAG GQETIDKVPI HTKDY UniProtKB: ATP synthase subunit epsilon, mitochondrial |
-Macromolecule #4: ATPase subunit 9, putative
Macromolecule | Name: ATPase subunit 9, putative / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.39887 KDa |
Sequence | String: MMRRLALQSS IRRATPFATP LVASTKALNP MCSAITIREA STVAISVQGL HYVGTGLAAI ALAGVGLGIG TIFGNLLVAC ARQPNLTKM LFNYAILGFA LTEAIGLFAL MLAFLMLFS UniProtKB: ATPase subunit 9, putative |
-Macromolecule #5: URIDINE 5'-TRIPHOSPHATE
Macromolecule | Name: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: UTP |
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Molecular weight | Theoretical: 484.141 Da |
Chemical component information | ![]() ChemComp-UTP: |
-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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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 33.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |