+Open data
-Basic information
Entry | Database: PDB / ID: 7y4l | ||||||
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Title | PBS of PBS-PSII-PSI-LHCs from Porphyridium purpureum. | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / PBS | ||||||
Function / homology | Function and homology information phycobilisome / chloroplast thylakoid membrane / photosynthesis / lyase activity / extracellular space Similarity search - Function | ||||||
Biological species | Porphyridium purpureum (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | You, X. / Zhang, X. / Cheng, J. / Xiao, Y.N. / Sun, S. / Sui, S.F. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2023 Title: In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex. Authors: Xin You / Xing Zhang / Jing Cheng / Yanan Xiao / Jianfei Ma / Shan Sun / Xinzheng Zhang / Hong-Wei Wang / Sen-Fang Sui / Abstract: In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red ...In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red algae consist of soluble phycobilisomes (PBSs) and transmembrane light-harvesting complexes (LHCs). Excitation energy transfer pathways from PBS to photosystems remain unclear owing to the lack of structural information. Here we present in situ structures of PBS-PSII-PSI-LHC megacomplexes from the red alga Porphyridium purpureum at near-atomic resolution using cryogenic electron tomography and in situ single-particle analysis, providing interaction details between PBS, PSII and PSI. The structures reveal several unidentified and incomplete proteins and their roles in the assembly of the megacomplex, as well as a huge and sophisticated pigment network. This work provides a solid structural basis for unravelling the mechanisms of PBS-PSII-PSI-LHC megacomplex assembly, efficient energy transfer from PBS to the two photosystems, and regulation of energy distribution between PSII and PSI. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y4l.cif.gz | 21.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7y4l.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7y4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y4l_validation.pdf.gz | 166.5 MB | Display | wwPDB validaton report |
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Full document | 7y4l_full_validation.pdf.gz | 158.2 MB | Display | |
Data in XML | 7y4l_validation.xml.gz | 3.9 MB | Display | |
Data in CIF | 7y4l_validation.cif.gz | 5 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/7y4l ftp://data.pdbj.org/pub/pdb/validation_reports/y4/7y4l | HTTPS FTP |
-Related structure data
Related structure data | 33605MC 7y1aC 7y5eC 7y7aC 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 , 9 types, 544 molecules AAEABACADAFAGAHAIALAMANAOAPAQARASAVAXAYAZAPBRBTBVBYBPCRCTCVC...
#1: Protein | Mass: 14749.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_1598 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YXP2 #2: Protein | Mass: 18584.182 Da / Num. of mol.: 276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpeB / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: P11393 #3: Protein | Mass: 17824.029 Da / Num. of mol.: 254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: peA, cpeA / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: E2IH77 #4: Protein | Mass: 28151.357 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_9475 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YJY8 #5: Protein | Mass: 35163.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_1715 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX67 #16: Protein | Mass: 16915.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_4247 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YTV6 #17: Protein | Mass: 30272.959 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_5140 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z2M2 #24: Protein | Mass: 99484.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcE / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A343KPB8 #30: Protein | Mass: 17273.779 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_5305 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z365 |
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-R-phycoerythrin gamma chain, ... , 4 types, 24 molecules ABACADAEAJYKY1A2A5A6AHA4w8x8wFxFBHB4y8yFMIZIM9Z9
#6: Protein | Mass: 31792.982 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2041 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX19 #12: Protein | Mass: 29453.639 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2042 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YZM7 #13: Protein | Mass: 31358.787 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2309 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YZH3 #14: Protein | Mass: 36924.992 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_9240 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YNU6 |
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-Phycobilisome ... , 9 types, 26 molecules BBBCBDBEB2B6XBXCXDXEX2X6MGZGe1eKX3z3b4bHd5dJb7Y7z8zF
#7: Protein | Mass: 26996.689 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpcG / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RZ90 #10: Protein | Mass: 39727.625 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_8023 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YM59 #11: Protein | Mass: 34958.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_0816 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z323 #15: Protein | Mass: 32886.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_7221 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z7F4 #23: Protein | Mass: 10428.983 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2818 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YVZ2 #25: Protein | Mass: 53601.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2314 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX63 #26: Protein | Mass: 36321.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_0729 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z162 #27: Protein | Mass: 45655.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_8365 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YMI8 #28: Protein | Mass: 55146.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_9810 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YI31 |
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-C-phycocyanin ... , 2 types, 72 molecules CBEBGBIBKBMBCCECGCICKCMCCDEDGDIDKDMDCEEEGEIEKEMEM2C2E2G2I2K2...
#8: Protein | Mass: 17478.664 Da / Num. of mol.: 36 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpcA / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RYI4 #9: Protein | Mass: 18242.705 Da / Num. of mol.: 36 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpcB / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RZB2 |
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-FAS1 domain-containing ... , 2 types, 4 molecules 43b3fAhA
#18: Protein | Mass: 26620.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_7258 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4ZA95 #29: Protein | Mass: 31332.955 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_0141 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z027 |
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-Allophycocyanin ... , 4 types, 46 molecules A3C3E3G3J3K3N3P3R3T3c3e3g3i3l3m3p3r3t3v3B3D3F3H3I3L3M3O3Q3S3...
#19: Protein | Mass: 17639.123 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcA / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RYM0 #20: Protein | Mass: 17415.797 Da / Num. of mol.: 22 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcB / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0S279 #21: Protein | Mass: 18126.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcD / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0S1U6 #22: Protein | Mass: 19778.740 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcF / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RZE2 |
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-Non-polymers , 3 types, 1602 molecules
#31: Chemical | ChemComp-PEB / #32: Chemical | ChemComp-PUB / #33: Chemical | ChemComp-CYC / |
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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: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: In situ PBS from Porphyridium purpureum / Type: CELL / Entity ID: #1-#30 / Source: RECOMBINANT |
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Source (natural) | Organism: Porphyridium purpureum (eukaryote) |
Source (recombinant) | Organism: Porphyridium purpureum (eukaryote) |
Buffer solution | pH: 7 |
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: 6000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215000 / Symmetry type: POINT |