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Yorodumi- PDB-7yca: Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreoco... -
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-Basic information
Entry | Database: PDB / ID: 7yca | |||||||||||||||
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Title | Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreococcus tauri | |||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Complex / Electron transport | |||||||||||||||
Function / homology | Function and homology information chloroplast photosystem I / 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 photosystem I / 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 / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Ostreococcus tauri (plant) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | |||||||||||||||
Authors | Shan, J. / Sheng, X. / Ishii, A. / Watanabe, A. / Song, C. / Murata, K. / Minagawa, J. / Liu, Z. | |||||||||||||||
Funding support | Japan, China, 4items
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Citation | Journal: Elife / Year: 2023 Title: The photosystem I supercomplex from a primordial green alga harbors three light-harvesting complex trimers. Authors: Asako Ishii / Jianyu Shan / Xin Sheng / Eunchul Kim / Akimasa Watanabe / Makio Yokono / Chiyo Noda / Chihong Song / Kazuyoshi Murata / Zhenfeng Liu / Jun Minagawa / Abstract: As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in ...As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of PSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll 603-609 pair in Lhca1-4. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yca.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7yca.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 7yca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/7yca ftp://data.pdbj.org/pub/pdb/validation_reports/yc/7yca | HTTPS FTP |
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-Related structure data
Related structure data | 33737MC 8hg3C 8hg5C 8hg6C 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
-Protein , 5 types, 5 molecules 16GLO
#1: Protein | Mass: 24128.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9U3 |
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#6: Protein | Mass: 26742.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A1Y5IA87 |
#13: Protein | Mass: 14124.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q019T9 |
#18: Protein | Mass: 21526.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A090M7B0 |
#21: Protein | Mass: 15020.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A096P9N0 |
-Chlorophyll a-b binding protein, ... , 6 types, 13 molecules 2345PRSTUVWXQ
#2: Protein | Mass: 26404.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A454XUD2 | ||
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#3: Protein | Mass: 29432.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9U5 | ||
#4: Protein | Mass: 25924.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9V1 | ||
#5: Protein | Mass: 23401.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A090M1L8 | ||
#22: Protein | Mass: 24689.807 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9U7 #23: Protein | | Mass: 24161.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A090LYE8 |
-Photosystem I ... , 12 types, 12 molecules ABCDEFHIJKMN
#7: Protein | Mass: 83249.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3K1, photosystem I |
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#8: Protein | Mass: 81421.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3K2, photosystem I |
#9: Protein | Mass: 8751.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3P1, photosystem I |
#10: Protein | Mass: 20560.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A1Y5I5Y8 |
#11: Protein | Mass: 11278.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A454XT75 |
#12: Protein | Mass: 24593.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q01B61 |
#14: Protein | Mass: 17797.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A096PAU9 |
#15: Protein/peptide | Mass: 3766.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3K0 |
#16: Protein/peptide | Mass: 4731.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3J4 |
#17: Protein | Mass: 13573.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A096P8E8 |
#19: Protein/peptide | Mass: 3413.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3J8 |
#20: Protein | Mass: 14405.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A090N3J0 |
-Sugars , 1 types, 2 molecules
#36: Sugar |
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-Non-polymers , 15 types, 451 molecules
#24: Chemical | ChemComp-CHL / #25: Chemical | ChemComp-CLA / #26: Chemical | ChemComp-IWJ / ( #27: Chemical | ChemComp-XAT / ( #28: Chemical | ChemComp-LHG / #29: Chemical | ChemComp-Q6L / ( #30: Chemical | ChemComp-BCR / #31: Chemical | ChemComp-LMG / #32: Chemical | #33: Chemical | ChemComp-CL0 / | #34: Chemical | #35: Chemical | #37: Chemical | ChemComp-NEX / ( |
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