+Open data
-Basic information
Entry | Database: PDB / ID: 6fkh | ||||||
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Title | Chloroplast F1Fo conformation 2 | ||||||
Components | (ATP synthase ...) x 9 | ||||||
Keywords | MEMBRANE PROTEIN / ATP synthase / membrane protein complex / molecular motor | ||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / : / : / : / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II ...proton motive force-driven plasma membrane ATP synthesis / : / : / : / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / 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 motive force-driven mitochondrial ATP synthesis / ADP binding / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Hahn, A. / Vonck, J. / Mills, D.J. / Meier, T. / Kuehlbrandt, W. | ||||||
Citation | Journal: Science / Year: 2018 Title: Structure, mechanism, and regulation of the chloroplast ATP synthase. Authors: Alexander Hahn / Janet Vonck / Deryck J Mills / Thomas Meier / Werner Kühlbrandt / Abstract: The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through ...The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through the membrane-embedded F motor drive ATP synthesis in the F head by rotary catalysis. We determined the high-resolution structure of the complete cFF complex by cryo-electron microscopy, resolving side chains of all 26 protein subunits, the five nucleotides in the F head, and the proton pathway to and from the rotor ring. The flexible peripheral stalk redistributes differences in torsional energy across three unequal steps in the rotation cycle. Plant ATP synthase is autoinhibited by a β-hairpin redox switch in subunit γ that blocks rotation in the dark. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6fkh.cif.gz | 882.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fkh.ent.gz | 732.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fkh_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6fkh_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6fkh_validation.xml.gz | 129.6 KB | Display | |
Data in CIF | 6fkh_validation.cif.gz | 203.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fkh ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fkh | HTTPS FTP |
-Related structure data
Related structure data | 4271MC 4270C 4272C 4273C 6fkfC 6fkiC 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 ... , 9 types, 26 molecules aCEADFBegSNOPQRMTGHLKJIpbd
#1: Protein | Mass: 27102.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06451 | ||||||||||||||
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#2: Protein | Mass: 55505.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) References: UniProt: P06450, H+-transporting two-sector ATPase #3: Protein | Mass: 53797.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) References: UniProt: P00825, H+-transporting two-sector ATPase #4: Protein | | Mass: 14715.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P00833 #5: Protein | | Mass: 40119.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P05435 #6: Protein | Mass: 7977.366 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69447 #7: Protein | | Mass: 24487.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P31853 #8: Protein | | Mass: 21013.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06453 #9: Protein | | Mass: 27708.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P11402 |
-Non-polymers , 3 types, 10 molecules
#10: Chemical | ChemComp-MG / #11: Chemical | #12: Chemical | |
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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: Chloroplast ATP synthase / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.6 MDa | ||||||||||||||||||||
Source (natural) | Organism: Spinacia oleracea (spinach) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283 K |
-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 magnification: 75000 X / Calibrated magnification: 132953 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 62 sec. / Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 6254 |
-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 ONLY | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 670614 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15395 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: rigid body fit from structure build in complex in conformation 1 | ||||||||||||||||||||||||||||||||
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