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Yorodumi- PDB-8kde: Cryo-EM structure of an intermediate-state complex during the pro... -
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-Basic information
Entry | Database: PDB / ID: 8kde | ||||||||||||
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Title | Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / monomeric Photosystem II / PSII repair | ||||||||||||
Function / homology | Function and homology information photosystem II repair / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding ...photosystem II repair / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis / protein stabilization / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||
Authors | Li, A. / Wang, Y. / Liu, Z. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii. Authors: Anjie Li / Tingting You / Xiaojie Pang / Yidi Wang / Lijin Tian / Xiaobo Li / Zhenfeng Liu / Abstract: Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs ...Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs to be restored through a process known as the PSII repair cycle. The detailed molecular mechanism underlying the PSII repair process remains mostly elusive. Here, we report biochemical and structural features of a PSII-repair intermediate complex, likely arrested at an early stage of the PSII repair process in the green alga Chlamydomonas reinhardtii. The complex contains three protein factors associated with a damaged PSII core, namely Thylakoid Enriched Factor 14 (TEF14), Photosystem II Repair Factor 1 (PRF1), and Photosystem II Repair Factor 2 (PRF2). TEF14, PRF1 and PRF2 may facilitate the release of the manganese-stabilizing protein PsbO, disassembly of peripheral light-harvesting complexes from PSII and blockage of the Q site, respectively. Moreover, an α-tocopherol quinone molecule is located adjacent to the heme group of cytochrome b, potentially fulfilling a photoprotective role by preventing the generation of reactive oxygen species. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kde.cif.gz | 507 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kde.ent.gz | 421.5 KB | Display | PDB format |
PDBx/mmJSON format | 8kde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kde_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 8kde_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 8kde_validation.xml.gz | 98.5 KB | Display | |
Data in CIF | 8kde_validation.cif.gz | 132.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/8kde ftp://data.pdbj.org/pub/pdb/validation_reports/kd/8kde | HTTPS FTP |
-Related structure data
Related structure data | 37133MC 8zeeC 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
-Photosystem II ... , 14 types, 14 molecules BDHIKLMTVZ3CA1
#1: Protein | Mass: 56089.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A218N8S0 |
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#2: Protein | Mass: 39474.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P06007, photosystem II |
#5: Protein | Mass: 9445.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P22666 |
#6: Protein/peptide | Mass: 4245.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59763 |
#7: Protein/peptide | Mass: 5062.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P18263 |
#8: Protein/peptide | Mass: 4431.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P32974 |
#9: Protein/peptide | Mass: 3762.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P92277 |
#10: Protein/peptide | Mass: 3639.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P37256 |
#11: Protein/peptide | Mass: 3333.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P50370 |
#13: Protein | Mass: 6565.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P92276 |
#15: Protein | Mass: 13340.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DWM2 |
#16: Protein | Mass: 50680.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P10898 |
#17: Protein | Mass: 39066.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P07753, photosystem II |
#18: Protein | Mass: 12002.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HNG8 |
-Cytochrome b559 subunit ... , 2 types, 2 molecules EF
#3: Protein | Mass: 9312.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P48268 |
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#4: Protein/peptide | Mass: 4986.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q08363 |
-Protein , 2 types, 2 molecules XG
#12: Protein | Mass: 9894.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I846 |
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#14: Protein | Mass: 20601.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HY43 |
-Sugars , 1 types, 3 molecules
#27: Sugar |
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-Non-polymers , 11 types, 69 molecules
#19: Chemical | ChemComp-CLA / #20: Chemical | ChemComp-BCR / #21: Chemical | ChemComp-LMG / #22: Chemical | ChemComp-LHG / #23: Chemical | ChemComp-PL9 / | #24: Chemical | #25: Chemical | ChemComp-HEM / | #26: Chemical | ChemComp-VTQ / | #28: Chemical | ChemComp-SQD / | #29: Chemical | ChemComp-BCT / | #30: Chemical | ChemComp-FE2 / | |
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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: Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Organelle: chloroplast |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 510932 / Symmetry type: POINT |