+Open data
-Basic information
Entry | Database: PDB / ID: 6cp6 | |||||||||
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Title | Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc. | |||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / ATP synthase | |||||||||
Function / homology | Function and homology information : / : / : / cristae formation / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / : ...: / : / : / cristae formation / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / : / : / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / ADP binding / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Srivastava, A.P. / Luo, M. / Symersky, J. / Liao, M.F. / Mueller, D.M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2018 Title: High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane. Authors: Anurag P Srivastava / Min Luo / Wenchang Zhou / Jindrich Symersky / Dongyang Bai / Melissa G Chambers / José D Faraldo-Gómez / Maofu Liao / David M Mueller / Abstract: Mitochondrial adenosine triphosphate (ATP) synthase comprises a membrane embedded F motor that rotates to drive ATP synthesis in the F subunit. We used single-particle cryo-electron microscopy (cryo- ...Mitochondrial adenosine triphosphate (ATP) synthase comprises a membrane embedded F motor that rotates to drive ATP synthesis in the F subunit. We used single-particle cryo-electron microscopy (cryo-EM) to obtain structures of the full complex in a lipid bilayer in the absence or presence of the inhibitor oligomycin at 3.6- and 3.8-angstrom resolution, respectively. To limit conformational heterogeneity, we locked the rotor in a single conformation by fusing the F6 subunit of the stator with the δ subunit of the rotor. Assembly of the enzyme with the F6-δ fusion caused a twisting of the rotor and a 9° rotation of the F c-ring in the direction of ATP synthesis, relative to the structure of isolated F Our cryo-EM structures show how F and F are coupled, give insight into the proton translocation pathway, and show how oligomycin blocks ATP synthesis. | |||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6cp6.cif.gz | 857.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cp6.ent.gz | 704.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cp6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6cp6_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6cp6_validation.xml.gz | 137.2 KB | Display | |
Data in CIF | 6cp6_validation.cif.gz | 211.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/6cp6 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/6cp6 | HTTPS FTP |
-Related structure data
Related structure data | 7548MC 7546C 7547C 7549C 6cp3C 6cp5C 6cp7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ATP synthase subunit ... , 13 types, 26 molecules KLMNOPQRSTYABCDEFGHIZ76UXJ
#1: Protein | Mass: 7790.385 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P61829 #2: Protein | | Mass: 20901.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P09457 #3: Protein | Mass: 55007.402 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P07251 #4: Protein | Mass: 51181.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P00830, H+-transporting two-sector ATPase #5: Protein | | Mass: 30657.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38077 #6: Protein | | Mass: 14565.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12165 #7: Protein | | Mass: 6618.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P21306 #8: Protein | | Mass: 23194.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05626 #9: Protein | | Mass: 19709.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P30902 #10: Protein | | Mass: 10417.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12349 #11: Protein | | Mass: 10584.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q06405 #13: Protein | | Mass: 27900.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P00854 #14: Protein/peptide | | Mass: 4145.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P81450 |
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-Protein/peptide , 1 types, 1 molecules 8
#12: Protein/peptide | Mass: 5825.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P00856 |
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-Non-polymers , 2 types, 5 molecules
#15: Chemical | #16: Chemical | |
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-Details
Has protein modification | 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: Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc. Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: strain ATCC 204508 / S288c |
Buffer solution | pH: 8 / Details: 20 mM Tris-HCl, 150 mM NaCl, pH 8.0 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 91 % |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 31000 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2600 nm / Cs: 2 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 105 K / Temperature (min): 80 K |
Image recording | Electron dose: 8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 5935 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 541568 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160937 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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