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Open data
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Basic information
Entry | Database: PDB / ID: 8ap6 | ||||||
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Title | Trypanosoma brucei mitochondrial F1Fo ATP synthase dimer | ||||||
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![]() | MEMBRANE PROTEIN / ATP synthase / mitochondria | ||||||
Function / homology | ![]() H+-transporting two-sector ATPase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / : / : / : / : ...H+-transporting two-sector ATPase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / : / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial membrane / ADP binding / mitochondrial inner membrane / hydrolase activity / lipid binding / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Muehleip, A. / Gahura, O. / Zikova, A. / Amunts, A. | ||||||
Funding support | European Union, 1items
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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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 15559MC ![]() 8ap7C ![]() 8ap8C ![]() 8ap9C ![]() 8apaC ![]() 8apbC ![]() 8apcC ![]() 8apdC ![]() 8apeC ![]() 8apfC ![]() 8apgC ![]() 8aphC ![]() 8apjC ![]() 8apkC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-ATP synthase subunit ... , 5 types, 22 molecules AaA1A2B1B2C1C2D1D2E1E2F1F2I1I2J1J2K1K2L1L2
#1: Protein | Mass: 28708.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 63574.465 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 55836.879 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9GPE9, H+-transporting two-sector ATPase #13: Protein | Mass: 8706.890 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 21268.279 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 20 types, 58 molecules CcDdEeFfGgG1G2HhH1H2IiJjKkLlMmM1M2Nn...
#3: Protein | Mass: 13750.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 43379.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 46883.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 17182.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 27646.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 34472.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A161CM65, H+-transporting two-sector ATPase #10: Protein | Mass: 17218.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 20172.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q586H1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances #12: Protein | Mass: 12661.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 20307.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 14531.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 10448.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 16092.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 28869.924 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 17929.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein | Mass: 11676.294 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #22: Protein | Mass: 12398.870 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q38C84, H+-transporting two-sector ATPase #23: Protein | Mass: 12325.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #24: Protein | Mass: 12293.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #25: Protein | Mass: 7649.776 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 1 types, 4 molecules ![](data/chem/img/LMT.gif)
#30: Sugar | ChemComp-LMT / |
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-Non-polymers , 8 types, 62 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/Q7G.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/UTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/Q7G.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/UTP.gif)
#26: Chemical | ChemComp-ATP / #27: Chemical | ChemComp-MG / #28: Chemical | ChemComp-CDL / #29: Chemical | #31: Chemical | ChemComp-Q7G / #32: Chemical | ChemComp-PEE / #33: Chemical | ChemComp-PC1 / #34: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: mitochondrial ATP synthase dimer from Trypanosoma brucei Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#25 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K |
Image recording | Electron dose: 33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36925 / Symmetry type: POINT |
Atomic model building | Space: REAL |