+Open data
-Basic information
Entry | Database: PDB / ID: 7wyi | |||||||||
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Title | Native Photosystem I of Chlamydomonas reinhardtii | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / membrane supercomplex / light harvesting / electron transport / green algae | |||||||||
Function / homology | Function and homology information photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / photosynthetic electron transport in photosystem I / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / photosynthetic electron transport in photosystem I / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Kurisu, G. / Gerle, C. / Mitsuoka, K. / Kawamoto, A. / Tanaka, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2023 Title: Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin. Authors: Christoph Gerle / Yuko Misumi / Akihiro Kawamoto / Hideaki Tanaka / Hisako Kubota-Kawai / Ryutaro Tokutsu / Eunchul Kim / Dror Chorev / Kazuhiro Abe / Carol V Robinson / Kaoru Mitsuoka / Jun ...Authors: Christoph Gerle / Yuko Misumi / Akihiro Kawamoto / Hideaki Tanaka / Hisako Kubota-Kawai / Ryutaro Tokutsu / Eunchul Kim / Dror Chorev / Kazuhiro Abe / Carol V Robinson / Kaoru Mitsuoka / Jun Minagawa / Genji Kurisu / Abstract: Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural ...Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural characterization of soluble binding partners is less advanced. Here, we used X-ray crystallography and single particle cryo-EM to investigate three structures of the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. An X-ray structure demonstrates the absence of six chlorophylls from the luminal side of the LHCI belts, suggesting these pigments were either physically absent or less stably associated with the complex, potentially influencing excitation transfer significantly. CryoEM revealed extra densities on luminal and stromal sides of the supercomplex, situated in the vicinity of the electron transfer sites. These densities disappeared after the binding of oxidized ferredoxin to PSI-LHCI. Based on these structures, we propose the existence of a PSI-LHCI resting state with a reduced active chlorophyll content, electron donors docked in waiting positions and regulatory binding partners positioned at the electron acceptor site. The resting state PSI-LHCI supercomplex would be recruited to its active form by the availability of oxidized ferredoxin. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wyi.cif.gz | 690.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wyi.ent.gz | 525.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wyi_validation.pdf.gz | 12.4 MB | Display | wwPDB validaton report |
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Full document | 7wyi_full_validation.pdf.gz | 12.7 MB | Display | |
Data in XML | 7wyi_validation.xml.gz | 128.9 KB | Display | |
Data in CIF | 7wyi_validation.cif.gz | 186.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/7wyi ftp://data.pdbj.org/pub/pdb/validation_reports/wy/7wyi | HTTPS FTP |
-Related structure data
Related structure data | 32892MC 7wznC 8h2uC 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
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 83239.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12154, photosystem I |
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#2: Protein | Mass: 82184.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09144, photosystem I |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 8869.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q00914, photosystem I |
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-Photosystem I reaction center subunit ... , 4 types, 4 molecules DEFJ
#4: Protein | Mass: 21372.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39615 |
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#5: Protein | Mass: 10786.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12352 |
#6: Protein | Mass: 24088.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12356 |
#7: Protein/peptide | Mass: 4750.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59777 |
-Chlorophyll a-b binding protein, ... , 8 types, 8 molecules 1378Z456
#8: Protein | Mass: 23520.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7DM26 |
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#9: Protein | Mass: 32629.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JF10 |
#10: Protein | Mass: 26248.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q84Y02 |
#11: Protein | Mass: 25948.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY7 |
#12: Protein | Mass: 23923.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q05093 |
#13: Protein | Mass: 28729.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VZ0 |
#14: Protein | Mass: 28257.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY8 |
#15: Protein | Mass: 27812.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY6 |
-Non-polymers , 5 types, 171 molecules
#16: Chemical | ChemComp-CL0 / | ||||||
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#17: Chemical | ChemComp-CLA / #18: Chemical | #19: Chemical | #20: Chemical | ChemComp-CHL / |
-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: Native Photosystem I with bound Light Harvesting Complex I from Chlamydomonas reinhardtii thylakoid membranes. Type: COMPLEX Details: Membrane supercomplex purified without column use under green light conditions, stabilized by the mild detergent GDN with excess detergent removed using GraDeR. Entity ID: #1-#15 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.765 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Strain: Wild Type strain 137c / Cellular location: Thylakoid membrane / Organelle: Chloroplast | |||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was monodisperse with a low level of contaminants and excess free detergent removed using the GraDeR approach. | |||||||||||||||
Specimen support | Details: Both sides of the grid were glow discharged at 5 mA for 90 seconds. Grid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K Details: 2.6 microliter of sample were applied to cryo-grids and blotted for 4 seconds using Whatman #1 before plunge freezing. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: Preliminary grid screening was performed manually using a JEOL JEM-3000SFF microscope. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 45.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4080 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1410677 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47618 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6JO5 Accession code: 6JO5 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.9 Å |