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- PDB-8aph: rotational state 2c of the Trypanosoma brucei mitochondrial ATP s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8aph | ||||||
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Title | rotational state 2c of the Trypanosoma brucei mitochondrial ATP synthase dimer | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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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PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 15571MC ![]() 8ap6C ![]() 8ap7C ![]() 8ap8C ![]() 8ap9C ![]() 8apaC ![]() 8apbC ![]() 8apcC ![]() 8apdC ![]() 8apeC ![]() 8apfC ![]() 8apgC ![]() 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
-Protein , 20 types, 31 molecules LlMmcdefghijknopqrH1M1O1P1Q1R1S1T1U1V1W1X1G1
#1: Protein | Mass: 10448.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Protein | Mass: 16092.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #4: Protein | | Mass: 13750.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #5: Protein | | Mass: 43379.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #6: Protein | | Mass: 46883.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #7: Protein | | Mass: 17182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #8: Protein | | Mass: 27646.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #9: Protein | | Mass: 17218.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #10: Protein | | Mass: 12661.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #11: Protein | | Mass: 20307.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #12: Protein | | Mass: 14531.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #13: Protein | | Mass: 17929.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #14: Protein | | Mass: 11676.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #15: Protein | | Mass: 12325.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #16: Protein | | Mass: 12293.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #17: Protein | | Mass: 7649.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #18: Protein | | ![]() Mass: 20172.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: Q586H1, ![]() #21: Protein | | ![]() Mass: 28869.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #22: Protein | ![]() Mass: 12398.870 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: Q38C84, ![]() #23: Protein | | ![]() Mass: 34472.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: A0A161CM65, ![]() |
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-ATP synthase subunit ... , 5 types, 11 molecules aI1J1K1L1A1B1C1D1E1F1
#3: Protein | ![]() Mass: 28708.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() | ||||
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#19: Protein | ![]() Mass: 8706.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() | ||||
#20: Protein | ![]() Mass: 21268.279 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #24: Protein | ![]() Mass: 63574.465 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #25: Protein | ![]() Mass: 55836.879 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: Q9GPE9, ![]() |
-Sugars , 1 types, 2 molecules ![](data/chem/img/LMT.gif)
#28: Sugar |
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-Non-polymers , 8 types, 34 molecules ![](data/chem/img/CDL.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/Q7G.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/UTP.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/Q7G.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/UTP.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#26: Chemical | ChemComp-CDL / ![]() #27: Chemical | ![]() #29: Chemical | #30: Chemical | ChemComp-PC1 / ![]() #31: Chemical | ChemComp-UTP / | ![]() #32: Chemical | ChemComp-ATP / ![]() #33: Chemical | ChemComp-MG / #34: Chemical | ChemComp-ADP / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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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![]() ![]() |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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![]() ![]() |
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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11035 / Symmetry type: POINT |