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Yorodumi- PDB-6jo6: Structure of the green algal photosystem I supercomplex with ligh... -
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-Basic information
Entry | Database: PDB / ID: 6jo6 | ||||||||||||
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Title | Structure of the green algal photosystem I supercomplex with light-harvesting complex I | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem membrane protein | ||||||||||||
Function / homology | Function and homology information photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Suga, M. / Miyazaki, N. / Takahashi, Y. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Nat Plants / Year: 2019 Title: Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I. Authors: Michihiro Suga / Shin-Ichiro Ozawa / Kaori Yoshida-Motomura / Fusamichi Akita / Naoyuki Miyazaki / Yuichiro Takahashi / Abstract: In plants and green algae, the core of photosystem I (PSI) is surrounded by a peripheral antenna system consisting of light-harvesting complex I (LHCI). Here we report the cryo-electron ...In plants and green algae, the core of photosystem I (PSI) is surrounded by a peripheral antenna system consisting of light-harvesting complex I (LHCI). Here we report the cryo-electron microscopic structure of the PSI-LHCI supercomplex from the green alga Chlamydomonas reinhardtii. The structure reveals that eight Lhca proteins form two tetrameric LHCI belts attached to the PsaF side while the other two Lhca proteins form an additional Lhca2/Lhca9 heterodimer attached to the opposite side. The spatial arrangement of light-harvesting pigments reveals that Chlorophylls b are more abundant in the outer LHCI belt than in the inner LHCI belt and are absent from the core, thereby providing the downhill energy transfer pathways to the PSI core. PSI-LHCI is complexed with a plastocyanin on the patch of lysine residues of PsaF at the luminal side. The assembly provides a structural basis for understanding the mechanism of light-harvesting, excitation energy transfer of the PSI-LHCI supercomplex and electron transfer with plastocyanin. | ||||||||||||
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 | 6jo6.cif.gz | 1016.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jo6.ent.gz | 925.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jo6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/6jo6 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/6jo6 | HTTPS FTP |
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-Related structure data
Related structure data | 9854MC 9853C 9855C 9856C 6jo5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10314 (Title: Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I. Data size: 8.0 TB Data #1: Raw multiframe micrographs [micrographs - multiframe]) |
-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 genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: psaA, ps1a1 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: P12154, photosystem I |
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#2: Protein | Mass: 84947.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: psaB, ps1a2 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: P09144, photosystem I |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFGIJKL
#4: Protein | Mass: 17732.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: psaD / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: Q39615 |
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#5: Protein | Mass: 8135.226 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PSAE / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: P12352 |
#6: Protein | Mass: 17957.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PSAF / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: P12356 |
#7: Protein | Mass: 9828.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PSAG / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: P14224 |
#8: Protein | Mass: 10586.388 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PSAI / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8IFG7 |
#9: Protein/peptide | Mass: 4750.509 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: psaJ / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: P59777 |
#10: Protein | Mass: 8431.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PSAK / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: P14225 |
#11: Protein | Mass: 16120.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PSAL, CHLRE_12g486300v5, CHLREDRAFT_205935 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8IL32 |
-Chlorophyll a-b binding protein, ... , 7 types, 8 molecules 1Z378456
#12: Protein | Mass: 20368.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: cabI-1 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: Q7DM26, UniProt: Q05093*PLUS #13: Protein | | Mass: 29435.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: LHCA3, CHLREDRAFT_153678 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8JF10 #14: Protein | | Mass: 23446.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: Lhca, CHLRE_16g687900v5 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: Q84Y02 #15: Protein | | Mass: 23293.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: LhcI-4, LHCA8, CHLRE_06g272650v5, CHLREDRAFT_187025 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY7 #16: Protein | | Mass: 25906.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: LhcI-1, CHLRE_10g452050v5 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VZ0 #17: Protein | | Mass: 25264.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: LhcI-3, LHCA5, CHLRE_10g425900v5, CHLREDRAFT_186299 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY8 #18: Protein | | Mass: 25183.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: LhcI-5, LHCA6, CHLRE_06g278213v5, CHLREDRAFT_192961 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY6 |
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-Protein / Sugars , 2 types, 2 molecules C
#25: Sugar | ChemComp-DGD / |
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#3: Protein | Mass: 8869.325 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: psaC / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: Q00914, photosystem I |
-Non-polymers , 9 types, 284 molecules
#19: Chemical | ChemComp-CL0 / | ||||||||||||||
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#20: Chemical | ChemComp-CLA / #21: Chemical | #22: Chemical | ChemComp-LHG / #23: Chemical | ChemComp-BCR / #24: Chemical | #26: Chemical | ChemComp-LMG / | #27: Chemical | ChemComp-CHL / #28: Chemical | ChemComp-LUT / ( |
-Details
Sequence details | Authors made a transformant which bears 20 x His insertion in the N-terminal region. |
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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: Photosystem I - Light Harvesting Complex I supercomplex Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Source (recombinant) | Organism: Chlamydomonas reinhardtii (plant) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: MOLYBDENUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal defocus max: 3750 nm / Nominal defocus min: 1600 nm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 9801 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 379749 / Symmetry type: POINT |