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Yorodumi- PDB-9is4: Cryo-EM structure of a TEF30-associated intermediate C2S-type PSI... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9is4 | |||||||||||||||
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| Title | Cryo-EM structure of a TEF30-associated intermediate C2S-type PSII-LHCII supercomplex from Chlamydomonas reinhardtii | |||||||||||||||
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Keywords | PHOTOSYNTHESIS / photosystem II / PSII repair / PSII assembly / PSII intermediate / TEF30 / C2S / supercomplex | |||||||||||||||
| Function / homology | Function and homology informationthylakoid light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor ...thylakoid light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / : / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / response to light stimulus / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||||||||
| Biological species | ![]() | |||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
Authors | Wang, Y. / Wang, C. / Li, A. / Liu, Z. | |||||||||||||||
| Funding support | China, 1items
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Citation | Journal: Nat Plants / Year: 2025Title: Roles of multiple TEF30-associated intermediate complexes in the repair and reassembly of photosystem II in Chlamydomonas reinhardtii. Authors: Yidi Wang / Chenxi Wang / Anjie Li / Zhenfeng Liu / ![]() Abstract: During oxygenic photosynthesis, photosystem II (PSII) uses light energy for oxidizing water and reducing plastoquinone. It is susceptible to photodamage, and the damaged PSII is repaired through a ...During oxygenic photosynthesis, photosystem II (PSII) uses light energy for oxidizing water and reducing plastoquinone. It is susceptible to photodamage, and the damaged PSII is repaired through a sophisticated biological process assisted by numerous auxiliary proteins. Here we report the cryogenic electron microscopy structures of four PSII-repair complexes from Chlamydomonas reinhardtii associated with the Thylakoid Enriched Fraction 30 (TEF30, an orthologue of plant MET1) protein-namely, a TEF30-PSII core monomer (TEF30-C), two types of TEF30-PSII core dimers (types I and II, TEF30-C-I and TEF30-C-II) and a TEF30-CS-type PSII-LHCII supercomplex (TEF30-CS; S, strongly associated light-harvesting complex II trimer). TEF30 mediates the assembly of CP43 with the RC47 module by clamping on the stromal surfaces and prevents the premature association of peripheral antennae with PSII-C. In the transition from TEF30-C-I to TEF30-C-II, TEF30-CS and mature CS, one PSII core slides along the dimerization interface against the adjacent one by 22-35 Å, generating a zigzagged surface for accommodating the peripheral antennae. These results suggest that the PSII repair process undergoes multiple TEF30-mediated intermediate states to form intact PSII-LHCII supercomplexes. | |||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9is4.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9is4.ent.gz | 1.1 MB | Display | PDB format |
| PDBx/mmJSON format | 9is4.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9is4_validation.pdf.gz | 10.4 MB | Display | wwPDB validaton report |
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| Full document | 9is4_full_validation.pdf.gz | 11 MB | Display | |
| Data in XML | 9is4_validation.xml.gz | 228.1 KB | Display | |
| Data in CIF | 9is4_validation.cif.gz | 296.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/9is4 ftp://data.pdbj.org/pub/pdb/validation_reports/is/9is4 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 60830MC ![]() 9iiuC ![]() 9imnC ![]() 9ioxC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-Protein , 3 types, 3 molecules 1Or
| #1: Protein | Mass: 18299.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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| #15: Protein | Mass: 25704.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #23: Protein | Mass: 21906.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Photosystem II ... , 13 types, 25 molecules AaBbCcDdHhIiKkLlMmTtVvWZz
| #2: Protein | Mass: 37172.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 53051.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 49416.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 39342.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 7504.862 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein/peptide | Mass: 4016.790 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein/peptide | Mass: 4147.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein/peptide | Mass: 4300.033 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein/peptide | Mass: 3387.036 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein/peptide | Mass: 3510.259 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein/peptide | Mass: 3201.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | | Mass: 6158.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #22: Protein | Mass: 6466.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
| #6: Protein | Mass: 8598.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein/peptide | Mass: 3535.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Chlorophyll a-b binding protein, ... , 4 types, 4 molecules GNSY
| #8: Protein | Mass: 23561.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #14: Protein | Mass: 23648.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #16: Protein | Mass: 26767.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #21: Protein | Mass: 23808.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 1 types, 2 molecules Xx
| #20: Protein/peptide | Mass: 3056.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 2 types, 12 molecules 


| #31: Sugar | ChemComp-DGD / #32: Sugar | ChemComp-LMU / |
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-Non-polymers , 14 types, 211 molecules 


























| #24: Chemical | | #25: Chemical | ChemComp-CLA / #26: Chemical | ChemComp-PHO / #27: Chemical | ChemComp-BCR / #28: Chemical | #29: Chemical | ChemComp-LMG / #30: Chemical | ChemComp-LHG / #33: Chemical | #34: Chemical | #35: Chemical | #36: Chemical | ChemComp-CHL / #37: Chemical | ChemComp-LUT / ( #38: Chemical | ChemComp-NEX / ( #39: Chemical | ChemComp-XAT / ( |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | N |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: TEF30-associated C2S-type PSII-LHCII supercomplex / Type: COMPLEX / Entity ID: #2-#23 / Source: NATURAL |
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| Source (natural) | Organism: ![]() |
| Buffer solution | pH: 7.2 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Vitrification | Cryogen name: ETHANE |
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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: 1800 nm / Nominal defocus min: 1300 nm |
| Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
| CTF correction | Type: PHASE FLIPPING ONLY |
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| 3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97962 / Symmetry type: POINT |
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