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Yorodumi- PDB-8r2i: Cryo-EM Structure of native Photosystem II assembly intermediate ... -
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-Basic information
Entry | Database: PDB / ID: 8r2i | ||||||
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Title | Cryo-EM Structure of native Photosystem II assembly intermediate from Chlamydomonas reinhardtii | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem II / biogenesis of PSII / assembly intermediate / CryoEM / assembly factor / Chlamydomonas reinhardtii | ||||||
Function / homology | Function and homology information photosystem II repair / chloroplast thylakoid lumen / photosystem II assembly / oxygen evolving activity / 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 ...photosystem II repair / chloroplast thylakoid lumen / photosystem II assembly / oxygen evolving activity / 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 / chloroplast thylakoid membrane / phosphate ion binding / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Fadeeva, M. / Klaiman, D. / Kandiah, E. / Nelson, N. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Front Plant Sci / Year: 2023 Title: Structure of native photosystem II assembly intermediate from . Authors: Mariia Fadeeva / Daniel Klaiman / Eaazhisai Kandiah / Nathan Nelson / Abstract: Photosystem II (PSII) is a dimer consisting of at least 13 nuclear-encoded and four chloroplast-encoded protein subunits that collectively function as a sunlight-driven oxidoreductase. In this ... Photosystem II (PSII) is a dimer consisting of at least 13 nuclear-encoded and four chloroplast-encoded protein subunits that collectively function as a sunlight-driven oxidoreductase. In this study, we present the inaugural structure of a green alga PSII assembly intermediate (pre-PSII-int). This intermediate was isolated from chloroplast membranes of the temperature-sensitive mutant TSP4, cultivated for 14 hours at a non-permissive temperature. The assembly state comprises a monomer containing subunits A, B, C, D, E, F, H, I, K, and two novel assembly factors, Psb1 and Psb2. Psb1 is identified as a novel transmembrane helix located adjacent to PsbE and PsbF (cytochrome b559). The absence of PsbJ, typically found in mature PSII close to this position, indicates that Psb1 functions as an assembly factor. Psb2 is an eukaryotic homolog of the cyanobacterial assembly factor Psb27. The presence of iron, coupled with the absence of Q, Q, and the manganese cluster, implies a protective mechanism against photodamage and provides insights into the intricate assembly process. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r2i.cif.gz | 467 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r2i.ent.gz | 341.7 KB | Display | PDB format |
PDBx/mmJSON format | 8r2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r2i_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 8r2i_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 8r2i_validation.xml.gz | 103.3 KB | Display | |
Data in CIF | 8r2i_validation.cif.gz | 135.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/8r2i ftp://data.pdbj.org/pub/pdb/validation_reports/r2/8r2i | HTTPS FTP |
-Related structure data
Related structure data | 18848MC 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 ... , 8 types, 8 molecules ABCDHIK1
#1: Protein | Mass: 36287.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P07753, photosystem II |
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#2: Protein | Mass: 53739.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P37255 |
#3: Protein | Mass: 46468.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P10898 |
#4: Protein | Mass: 39241.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P06007, photosystem II |
#7: Protein | Mass: 7063.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P22666 |
#8: Protein/peptide | Mass: 3276.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P59763 |
#9: Protein/peptide | Mass: 4147.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P18263 |
#11: Protein/peptide | Mass: 3219.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P50370 |
-Cytochrome b559 subunit ... , 2 types, 2 molecules EF
#5: Protein | Mass: 8727.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: P48268 |
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#6: Protein/peptide | Mass: 3795.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: Q08363 |
-Protein , 1 types, 1 molecules 2
#10: Protein | Mass: 11213.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane / References: UniProt: A8I5A0 |
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-Sugars , 3 types, 6 molecules
#16: Sugar | #18: Sugar | #20: Sugar | ChemComp-DGD / | |
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-Non-polymers , 10 types, 57 molecules
#12: Chemical | ChemComp-FE2 / | ||||||||||||||||
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#13: Chemical | ChemComp-CLA / #14: Chemical | #15: Chemical | ChemComp-BCR / #17: Chemical | #19: Chemical | ChemComp-LHG / | #21: Chemical | ChemComp-BCT / | #22: Chemical | ChemComp-PL9 / | #23: Chemical | ChemComp-HEM / | #24: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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 II assembly intermediate from Chlamydomonas reinhardtii Type: COMPLEX / Entity ID: #1-#9, #11, #10 / Source: NATURAL |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Cellular location: thylakoid membrane |
Buffer solution | pH: 6 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K |
-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 magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.8 sec. / Electron dose: 1.07 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 25758 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 6408350 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 327737 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.69 Å2 | ||||||||||||||||||||||||||||
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