+Open data
-Basic information
Entry | Database: PDB / ID: 7y7b | ||||||
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Title | Cryo-EM structure of cryptophyte photosystem I | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Cryptophyte / Photosystem I / evolution | ||||||
Function / homology | Function and homology information thylakoid membrane / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / plastid / chloroplast thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / plastid / chloroplast thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Chroomonas placoidea (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å | ||||||
Authors | Zhao, L.S. / Li, K. / Zhang, Y.Z. / Liu, L.N. | ||||||
Funding support | China, 1items
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Citation | Journal: Plant Cell / Year: 2023 Title: Structural basis and evolution of the photosystem I-light-harvesting supercomplex of cryptophyte algae. Authors: Long-Sheng Zhao / Peng Wang / Kang Li / Quan-Bao Zhang / Fei-Yu He / Chun-Yang Li / Hai-Nan Su / Xiu-Lan Chen / Lu-Ning Liu / Yu-Zhong Zhang / Abstract: Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) ...Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) as light-harvesting complexes (LHCs). Here, we report the structure of the photosynthetic PSI-ACPI supercomplex from the cryptophyte Chroomonas placoidea at 2.7-Å resolution obtained by crygenic electron microscopy. Cryptophyte PSI-ACPI represents a unique PSI-LHCI intermediate in the evolution from red algal to diatom PSI-LHCI. The PSI-ACPI supercomplex is composed of a monomeric PSI core containing 14 subunits, 12 of which originated in red algae, 1 diatom PsaR homolog, and an additional peptide. The PSI core is surrounded by 14 ACPI subunits that form 2 antenna layers: an inner layer with 11 ACPIs surrounding the PSI core and an outer layer containing 3 ACPIs. A pigment-binding subunit that is not present in any other previously characterized PSI-LHCI complexes, ACPI-S, mediates the association and energy transfer between the outer and inner ACPIs. The extensive pigment network of PSI-ACPI ensures efficient light harvesting, energy transfer, and dissipation. Overall, the PSI-LHCI structure identified in this study provides a framework for delineating the mechanisms of energy transfer in cryptophyte PSI-LHCI and for understanding the evolution of photosynthesis in the red lineage, which occurred via secondary endosymbiosis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y7b.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7y7b.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7y7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y7b_validation.pdf.gz | 20.5 MB | Display | wwPDB validaton report |
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Full document | 7y7b_full_validation.pdf.gz | 21.5 MB | Display | |
Data in XML | 7y7b_validation.xml.gz | 270.2 KB | Display | |
Data in CIF | 7y7b_validation.cif.gz | 333 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/7y7b ftp://data.pdbj.org/pub/pdb/validation_reports/y7/7y7b | HTTPS FTP |
-Related structure data
Related structure data | 33659MC 7y8aC 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 , 18 types, 19 molecules 123456789CORXZadbce
#1: Protein | Mass: 23479.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
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#2: Protein | Mass: 23400.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#3: Protein | Mass: 24966.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#4: Protein | Mass: 23548.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#5: Protein | Mass: 24055.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#6: Protein | Mass: 22688.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#7: Protein | Mass: 24550.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#8: Protein | Mass: 23700.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#9: Protein | Mass: 23223.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#12: Protein | Mass: 8743.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI25, photosystem I | ||||||
#21: Protein | Mass: 10766.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#22: Protein | Mass: 13867.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#23: Protein | Mass: 13975.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#24: Protein | Mass: 25645.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) | ||||||
#25: Protein | Mass: 22270.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) #26: Protein | | Mass: 23755.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) #27: Protein | | Mass: 27212.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) #28: Protein | | Mass: 22451.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) |
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#10: Protein | Mass: 83493.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIB4, photosystem I |
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#11: Protein | Mass: 82219.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI95, photosystem I |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJKLM
#13: Protein | Mass: 15590.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIA6 |
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#14: Protein | Mass: 7352.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIF3 |
#15: Protein | Mass: 20393.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI52 |
#16: Protein/peptide | Mass: 3975.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI78 |
#17: Protein/peptide | Mass: 4862.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI55 |
#18: Protein | Mass: 8836.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI34 |
#19: Protein | Mass: 16490.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI68 |
#20: Protein/peptide | Mass: 3247.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI28 |
-Sugars , 2 types, 7 molecules
#38: Sugar | ChemComp-LMU / #41: Sugar | |
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-Non-polymers , 11 types, 410 molecules
#29: Chemical | ChemComp-CLA / #30: Chemical | ChemComp-KC2 / #31: Chemical | ChemComp-II0 / ( #32: Chemical | #33: Chemical | ChemComp-IHT / ( #34: Chemical | ChemComp-LMG / #35: Chemical | ChemComp-LHG / #36: Chemical | #37: Chemical | ChemComp-8CT / ( #39: Chemical | #40: Chemical | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-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 of cryptophyte / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL |
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Molecular weight | Value: 0.89 MDa / Experimental value: NO |
Source (natural) | Organism: Chroomonas placoidea (eukaryote) |
Buffer solution | pH: 6.5 |
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133521 / Symmetry type: POINT |