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Yorodumi- PDB-9phw: Structure of a mutated PSII complex that slows O-O bond formation... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9phw | |||||||||||||||||||||||||||
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| Title | Structure of a mutated PSII complex that slows O-O bond formation by perturbing the proton transfer pathway | |||||||||||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem II / water oxidation / oxygen-evolving complex / D1-V185N | |||||||||||||||||||||||||||
| Function / homology | Function and homology informationplasma membrane-derived thylakoid photosystem II / 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 II ...plasma membrane-derived thylakoid photosystem II / 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 II / response to herbicide / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / : / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding / identical protein binding Similarity search - Function | |||||||||||||||||||||||||||
| Biological species | ![]() | |||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.99 Å | |||||||||||||||||||||||||||
Authors | Flesher, D.A. / Debus, R.J. / Brudvig, G.W. | |||||||||||||||||||||||||||
| Funding support | United States, 1items
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Citation | Journal: To Be PublishedTitle: Structure of a mutated PSII complex that slows O-O bond formation by perturbing the proton transfer pathway Authors: Flesher, D.A. / Debus, R.J. / Brudvig, G.W. | |||||||||||||||||||||||||||
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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 | 9phw.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9phw.ent.gz | 1.1 MB | Display | PDB format |
| PDBx/mmJSON format | 9phw.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9phw_validation.pdf.gz | 8.5 MB | Display | wwPDB validaton report |
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| Full document | 9phw_full_validation.pdf.gz | 8.8 MB | Display | |
| Data in XML | 9phw_validation.xml.gz | 183 KB | Display | |
| Data in CIF | 9phw_validation.cif.gz | 227.8 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/9phw ftp://data.pdbj.org/pub/pdb/validation_reports/ph/9phw | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 71652MC 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
-Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoRrTtUuXx...
| #1: Protein | Mass: 38295.500 Da / Num. of mol.: 2 / Mutation: V185N / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 55954.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 50344.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 39519.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 7120.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein/peptide | Mass: 4338.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein/peptide | Mass: 3470.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein/peptide | Mass: 5114.127 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein/peptide | Mass: 4476.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein/peptide | Mass: 3910.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | Mass: 29939.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein/peptide | Mass: 4204.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein/peptide | Mass: 3571.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | Mass: 14256.163 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein/peptide | Mass: 4189.036 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #20: Protein/peptide | Mass: 4143.993 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #21: Protein | Mass: 6736.161 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
| #5: Protein | Mass: 9454.577 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein/peptide | Mass: 4935.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein , 2 types, 4 molecules QqVv
| #14: Protein | Mass: 16494.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | Mass: 17901.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 2 types, 70 molecules 


| #31: Sugar | ChemComp-LMT / #34: Sugar | ChemComp-DGD / |
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-Non-polymers , 15 types, 1176 molecules 




























| #22: Chemical | | #23: Chemical | #24: Chemical | ChemComp-CL / #25: Chemical | ChemComp-CLA / #26: Chemical | ChemComp-PHO / #27: Chemical | ChemComp-BCR / #28: Chemical | ChemComp-LMG / #29: Chemical | ChemComp-PL9 / #30: Chemical | ChemComp-SQD / #32: Chemical | #33: Chemical | ChemComp-LHG / #35: Chemical | ChemComp-HEM / #36: Chemical | #37: Chemical | ChemComp-CA / #38: Water | ChemComp-HOH / | |
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-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 |
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Sample preparation
| Component | Name: photosystem II / Type: COMPLEX Details: photosystem II containing the V185N substitution on the D1 subunit Entity ID: #1-#21 / Source: NATURAL |
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| Molecular weight | Experimental value: NO |
| Source (natural) | Organism: ![]() |
| Buffer solution | pH: 6.8 |
| 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: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
| Image recording | Electron dose: 49.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
| Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||
| 3D reconstruction | Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72628 / Symmetry type: POINT |
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FIELD EMISSION GUN