+Open data
-Basic information
Entry | Database: PDB / ID: 8wgh | ||||||
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Title | Cryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Complex | ||||||
Function / homology | Function and homology information plastoglobule / chloroplast thylakoid / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / photosynthetic electron transport in photosystem I / chlorophyll binding / chloroplast thylakoid membrane ...plastoglobule / chloroplast thylakoid / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / photosynthetic electron transport in photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Fittonia albivenis (plant) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||
Authors | Huang, G.Q. / Li, X.X. / Sui, S.F. / Qin, X.C. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure of the red-shifted Fittonia albivenis photosystem I. Authors: Xiuxiu Li / Guoqiang Huang / Lixia Zhu / Chenyang Hao / Sen-Fang Sui / Xiaochun Qin / Abstract: Photosystem I (PSI) from Fittonia albivenis, an Acanthaceae ornamental plant, is notable among green plants for its red-shifted emission spectrum. Here, we solved the structure of a PSI-light ...Photosystem I (PSI) from Fittonia albivenis, an Acanthaceae ornamental plant, is notable among green plants for its red-shifted emission spectrum. Here, we solved the structure of a PSI-light harvesting complex I (LHCI) supercomplex from F. albivenis at 2.46-Å resolution using cryo-electron microscopy. The supercomplex contains a core complex of 14 subunits and an LHCI belt with four antenna subunits (Lhca1-4) similar to previously reported angiosperm PSI-LHCI structures; however, Lhca3 differs in three regions surrounding a dimer of low-energy chlorophylls (Chls) termed red Chls, which absorb far-red beyond visible light. The unique amino acid sequences within these regions are exclusively shared by plants with strongly red-shifted fluorescence emission, suggesting candidate structural elements for regulating the energy state of red Chls. These results provide a structural basis for unraveling the mechanisms of light harvest and transfer in PSI-LHCI of under canopy plants and for designing Lhc to harness longer-wavelength light in the far-red spectral range. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wgh.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wgh.ent.gz | 912.4 KB | Display | PDB format |
PDBx/mmJSON format | 8wgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wgh_validation.pdf.gz | 9.9 MB | Display | wwPDB validaton report |
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Full document | 8wgh_full_validation.pdf.gz | 10.4 MB | Display | |
Data in XML | 8wgh_validation.xml.gz | 148.2 KB | Display | |
Data in CIF | 8wgh_validation.cif.gz | 183.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/8wgh ftp://data.pdbj.org/pub/pdb/validation_reports/wg/8wgh | HTTPS FTP |
-Related structure data
Related structure data | 37513MC 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
-Chlorophyll a-b binding protein ... , 4 types, 4 molecules 1234
#1: Protein | Mass: 26773.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
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#2: Protein | Mass: 28533.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
#3: Protein | Mass: 29766.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
#4: Protein | Mass: 27510.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#5: Protein | Mass: 83138.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A8A0WPY6. Source: (natural) Fittonia albivenis (plant) / References: UniProt: A0A8A0WPY6, photosystem I |
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#6: Protein | Mass: 82472.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id G9IB61. Source: (natural) Fittonia albivenis (plant) / References: UniProt: G9IB61, photosystem I |
-Protein , 1 types, 1 molecules C
#7: Protein | Mass: 9049.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A4QJG7. Source: (natural) Fittonia albivenis (plant) / References: UniProt: A4QJG7, photosystem I |
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-Photosystem I reaction center subunit ... , 11 types, 11 molecules DEFGHIJKLNO
#8: Protein | Mass: 21036.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
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#9: Protein | Mass: 16282.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
#10: Protein | Mass: 24203.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q9SHE8. Source: (natural) Fittonia albivenis (plant) / References: UniProt: Q9SHE8 |
#11: Protein | Mass: 15873.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
#12: Protein | Mass: 15201.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
#13: Protein/peptide | Mass: 3930.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A8A9WIB9. Source: (natural) Fittonia albivenis (plant) / References: UniProt: A0A8A9WIB9 |
#14: Protein/peptide | Mass: 5029.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q3C1K9. Source: (natural) Fittonia albivenis (plant) / References: UniProt: Q3C1K9 |
#15: Protein | Mass: 13435.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
#16: Protein | Mass: 23094.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
#17: Protein | Mass: 18673.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
#18: Protein | Mass: 15404.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant) |
-Sugars , 3 types, 13 molecules
#26: Sugar | ChemComp-HTG / #29: Sugar | #30: Sugar | ChemComp-DGD / | |
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-Non-polymers , 9 types, 212 molecules
#19: Chemical | ChemComp-CHL / #20: Chemical | ChemComp-CLA / #21: Chemical | ChemComp-LUT / ( #22: Chemical | ChemComp-XAT / ( #23: Chemical | ChemComp-BCR / #24: Chemical | ChemComp-LHG / #25: Chemical | #27: Chemical | #28: Chemical | |
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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: Photosystem I complex / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Source (natural) | Organism: Fittonia albivenis (plant) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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 FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157342 / Symmetry type: POINT | ||||||||||||||||||||||||
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