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Open data
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Basic information
Entry | Database: PDB / ID: 6z1r | |||||||||
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Title | bovine ATP synthase F1-peripheral stalk domain, state 2 | |||||||||
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![]() | HYDROLASE / ATP synthase / mitochondria / mammalian / complex | |||||||||
Function / homology | ![]() angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / proton-transporting ATP synthase complex / heme biosynthetic process / : ...angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / proton-transporting ATP synthase complex / heme biosynthetic process / : / : / : / : / Mitochondrial protein degradation / : / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven 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 / erythrocyte differentiation / proton motive force-driven mitochondrial ATP synthesis / aerobic respiration / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
![]() | Spikes, T. / Montgomery, M.G. / Walker, J.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the dimeric ATP synthase from bovine mitochondria. Authors: Tobias E Spikes / Martin G Montgomery / John E Walker / ![]() Abstract: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 128.8 KB | Display | |
Data in CIF | ![]() | 194.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11039MC ![]() 6yy0C ![]() 6z1uC ![]() 6zbbC ![]() 6zg7C ![]() 6zg8C ![]() 6zikC ![]() 6ziqC ![]() 6zitC ![]() 6ziuC ![]() 6zmrC ![]() 6znaC ![]() 6zpoC ![]() 6zqmC ![]() 6zqnC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-ATP synthase subunit ... , 6 types, 10 molecules ABCDEFGHIS
#1: Protein | Mass: 55302.191 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: In chains ABC, Glu 1 is technically correct. The DNA sequence for this protein encodes GLU. The actual residue is pyroGLU. However pyroGLU and pyroGLN are the same. Residue 481 in chains A, ...Details: In chains ABC, Glu 1 is technically correct. The DNA sequence for this protein encodes GLU. The actual residue is pyroGLU. However pyroGLU and pyroGLN are the same. Residue 481 in chains A, B, and C can be Gly or SER. e.g. in this structure should be GLY. We have used the following REMARK in other PDB files: REMARK 999 REFERENCE FOR THE ALPHA SUBUNIT J. E. WALKER, S. J. REMARK 999 POWELL,O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY,VOL 28,PP REMARK 999 4702-4708, 1989. REMARK 999 REMARK 999 SER 481 GLY IN CHAINS A, B AND C REMARK 999 WAS IDENTIFIED AS A GLY FROM THE PROTEIN REMARK 999 SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS REMARK 999 RESIDUE WAS AGC SER IN THREE CLONES WHILE IN TWO REMARK 999 OTHERS IT WAS GGC GLY. THE DIFFERENCE WAS THOUGHT TO REMARK 999 BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION REMARK 999 OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 REMARK 999 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN REMARK 999 THIS POSITION. Source: (natural) ![]() ![]() #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: The mature protein starts AAQA. UNIPROT are updating P00829 accordingly. Source: (natural) ![]() ![]() References: UniProt: P00829, H+-transporting two-sector ATPase #3: Protein | | Mass: 30300.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein/peptide | | Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | Mass: 20959.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 2 types, 2 molecules Jh
#6: Protein | Mass: 7462.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ATP synthase inhibitor protein IF1 Residues 1-60 with 6His affinity tag. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#10: Protein | Mass: 8971.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-ATP synthase F(0) complex subunit ... , 2 types, 9 molecules KLMNOPQRb
#7: Protein | Mass: 7653.034 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: Trimethyl-lysine at position 43 / Source: (natural) ![]() ![]() #9: Protein | | Mass: 24702.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 4 types, 28 molecules ![](data/chem/img/ATP.gif)
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![](data/chem/img/ADP.gif)
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#11: Chemical | #12: Chemical | ChemComp-MG / #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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
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Molecular weight |
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Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Nickel affinity purified filled by gel filtration | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294 K Details: The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting. |
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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 |
Image recording | Average exposure time: 12 sec. / Electron dose: 4.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90850 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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