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Yorodumi- PDB-8ap7: membrane region of the Trypanosoma brucei mitochondrial ATP synth... -
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-Basic information
Entry | Database: PDB / ID: 8ap7 | ||||||
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Title | membrane region of the Trypanosoma brucei mitochondrial ATP synthase dimer | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ATP synthase / mitochondria | ||||||
Function / homology | Function and homology information kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / mitochondrion ...kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / mitochondrion / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Muehleip, A. / Gahura, O. / Zikova, A. / Amunts, A. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nat Commun / Year: 2022 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ap7.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ap7.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8ap7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ap7_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 8ap7_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 8ap7_validation.xml.gz | 143 KB | Display | |
Data in CIF | 8ap7_validation.cif.gz | 199.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/8ap7 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/8ap7 | HTTPS FTP |
-Related structure data
Related structure data | 15560MC 8ap6C 8ap8C 8ap9C 8apaC 8apbC 8apcC 8apdC 8apeC 8apfC 8apgC 8aphC 8apjC 8apkC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 15 types, 30 molecules AaCcDdEeFfIiJjKkLlMmNnOoPpQqRr
#1: Protein | Mass: 28708.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P24499 #2: Protein | Mass: 13750.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q585K5 #3: Protein | Mass: 43379.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57ZW9 #4: Protein | Mass: 46883.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38CI8 #5: Protein | Mass: 17182.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57ZE2 #6: Protein | Mass: 12661.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57ZM4 #7: Protein | Mass: 20307.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A5R7 #8: Protein | Mass: 14531.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57VT0 #9: Protein | Mass: 10448.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q387J1 #10: Protein | Mass: 16092.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZJA0 #11: Protein | Mass: 17929.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q582T1 #12: Protein | Mass: 11676.294 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57Z84 #13: Protein | Mass: 12325.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZLR9 #14: Protein | Mass: 12293.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q583U4 #15: Protein | Mass: 7649.776 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister427 |
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-Sugars , 1 types, 4 molecules
#17: Sugar | ChemComp-LMT / |
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-Non-polymers , 5 types, 64 molecules
#16: Chemical | ChemComp-CDL / #18: Chemical | ChemComp-Q7G / #19: Chemical | ChemComp-PEE / #20: Chemical | ChemComp-PC1 / #21: Water | ChemComp-HOH / | |
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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 |
-Sample preparation
Component | Name: mitochondrial ATP synthase dimer from Trypanosoma brucei Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister427 / Organelle: Mitochondrion |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-Processing
Software | Name: PHENIX / Version: 1.19rc4_4035: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100605 / Symmetry type: POINT | ||||||||||||||||||||||||
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