+Open data
-Basic information
Entry | Database: PDB / ID: 8asp | ||||||||||||||||||
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Title | RCII/PSI complex, focused refinement of PSI | ||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem / assembly factor / membrane protein | ||||||||||||||||||
Function / homology | Function and homology information plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||
Authors | Zhao, Z. / Vercellino, I. / Knoppova, J. / Sobotka, R. / Murray, J.W. / Nixon, P.J. / Sazanov, L.A. / Komenda, J. | ||||||||||||||||||
Funding support | United Kingdom, European Union, Czech Republic, 5items
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Citation | Journal: Nat Commun / Year: 2023 Title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Authors: Ziyu Zhao / Irene Vercellino / Jana Knoppová / Roman Sobotka / James W Murray / Peter J Nixon / Leonid A Sazanov / Josef Komenda / Abstract: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly ...Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising MnCaO cluster, thereby preventing the premature binding of Mn and Ca ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the MnCaO cluster. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8asp.cif.gz | 620.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8asp.ent.gz | 537.3 KB | Display | PDB format |
PDBx/mmJSON format | 8asp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8asp_validation.pdf.gz | 8.9 MB | Display | wwPDB validaton report |
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Full document | 8asp_full_validation.pdf.gz | 9.1 MB | Display | |
Data in XML | 8asp_validation.xml.gz | 121.5 KB | Display | |
Data in CIF | 8asp_validation.cif.gz | 161.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/8asp ftp://data.pdbj.org/pub/pdb/validation_reports/as/8asp | HTTPS FTP |
-Related structure data
Related structure data | 15621MC 8am5C 8aslC C: citing same article (ref.) M: map data used to model this data |
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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 I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules ab
#1: Protein | Mass: 83036.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaA, slr1834 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P29254, photosystem I |
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#2: Protein | Mass: 81369.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaB, slr1835 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P29255, photosystem I |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules defijklm
#4: Protein | Mass: 15663.749 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaD, slr0737 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P19569 |
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#5: Protein | Mass: 8154.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaE, ssr2831 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P12975 |
#6: Protein | Mass: 18267.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaF, sll0819 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P29256 |
#7: Protein/peptide | Mass: 4414.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaI, smr0004 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: Q55330 |
#8: Protein/peptide | Mass: 4535.415 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaJ, sml0008 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: Q55329 |
#9: Protein | Mass: 8805.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaK1, psaK, ssr0390 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P72712 |
#10: Protein | Mass: 16631.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaL, slr1655 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P37277 |
#11: Protein/peptide | Mass: 3382.063 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaM, smr0005 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P72986 |
-Protein / Sugars , 2 types, 2 molecules c
#23: Sugar | ChemComp-LMT / |
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#3: Protein | Mass: 8837.261 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaC, ssl0563 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P32422, photosystem I |
-Non-polymers , 11 types, 133 molecules
#12: Chemical | ChemComp-CL0 / | ||||||||||||||||||
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#13: Chemical | ChemComp-CLA / #14: Chemical | #15: Chemical | ChemComp-BCR / #16: Chemical | ChemComp-LHG / #17: Chemical | ChemComp-LMG / #18: Chemical | ChemComp-45D / | #19: Chemical | #20: Chemical | #21: Chemical | ChemComp-EQ3 / ( | #22: Chemical | |
-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: RCII/PSI complex / Type: COMPLEX / Entity ID: #1-#8, #11 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: His-D2/DeltaCP47 |
Source (recombinant) | Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: His-D2/DeltaCP47 |
Buffer solution | pH: 6.5 |
Specimen | Conc.: 0.2 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 R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 90.9 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2853 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1250000 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178513 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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