+Open data
-Basic information
Entry | Database: PDB / ID: 8hg3 | |||||||||||||||
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Title | Cryo-EM structure of the Lhcp complex from Ostreococcus tauri | |||||||||||||||
Components | Chlorophyll a-b binding protein, chloroplastic | |||||||||||||||
Keywords | ELECTRON TRANSPORT / Complex / Light-harvesting / Photosynthesis | |||||||||||||||
Function / homology | Function and homology information photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane 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 | 8hg3.cif.gz | 193.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hg3.ent.gz | 173.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/8hg3 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/8hg3 | HTTPS FTP |
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-Related structure data
Related structure data | 34733MC 7ycaC 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 , 1 types, 3 molecules STU
#1: Protein | Mass: 24689.807 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ostreococcus tauri (plant) / Gene: OT_ostta16g00450 / Production host: Ostreococcus tauri (plant) / References: UniProt: Q3B9U7 |
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-Non-polymers , 6 types, 62 molecules
#2: Chemical | ChemComp-CLA / #3: Chemical | ChemComp-CHL / #4: Chemical | #5: Chemical | ChemComp-Q6L / ( #6: Chemical | #7: Chemical | ChemComp-IWJ / ( |
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-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: Prasinophyte-specific Lhc protein (Lhcp) complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Ostreococcus tauri (plant) / Strain: OTH95 / Cellular location: thylakoid membrane / Organelle: chloroplast | |||||||||||||||
Source (recombinant) | Organism: Ostreococcus tauri (plant) | |||||||||||||||
Buffer solution | pH: 6.5 / Details: 25mM MES-NaOH,pH 6.5 1% A8-35 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample is | |||||||||||||||
Specimen support | Details: none / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K / Details: Vitrification carried out in air atmosphere |
-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: 2200 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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Image processing | Details: The selected images were aligned by the beam-induced motion | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5288217 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80573 / Algorithm: BACK PROJECTION / Num. of class averages: 4 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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