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Yorodumi- PDB-9hei: Universal Photosystem II Intermediate with Light-Dependent Water-... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9hei | ||||||||||||||||||||||||
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| Title | Universal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Chlamydomonas reinhardtii | ||||||||||||||||||||||||
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Keywords | PHOTOSYNTHESIS / Green alga / PSII / Chlamydomonas reinhardtii / membrane protein / Cryo-EM / assembly intermediate / water-ferrocyanide oxido-reductase. | ||||||||||||||||||||||||
| Function / homology | Function and homology informationphotosystem II repair / chloroplast thylakoid lumen / 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 repair / chloroplast thylakoid lumen / 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 / extrinsic component of membrane / response to herbicide / chlorophyll binding / : / photosynthetic electron transport in photosystem II / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
| Biological species | ![]() | ||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||||||||||||||||||||
Authors | Nelson, N. / Klaiman, D. / Fadeeva, M. / Kandiah, E. | ||||||||||||||||||||||||
| Funding support | Israel, 1items
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Citation | Journal: To Be PublishedTitle: Universal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Chlamydomonas reinhardtii Authors: Nelson, N. / Klaiman, D. / Fadeeva, M. / Kandiah, E. | ||||||||||||||||||||||||
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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 | 9hei.cif.gz | 569.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9hei.ent.gz | 463.5 KB | Display | PDB format |
| PDBx/mmJSON format | 9hei.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9hei_validation.pdf.gz | 5 MB | Display | wwPDB validaton report |
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| Full document | 9hei_full_validation.pdf.gz | 5.3 MB | Display | |
| Data in XML | 9hei_validation.xml.gz | 138.7 KB | Display | |
| Data in CIF | 9hei_validation.cif.gz | 185.9 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/9hei ftp://data.pdbj.org/pub/pdb/validation_reports/he/9hei | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 52077MC 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 ... , 15 types, 15 molecules ABVCDHIJKLMTZUW
| #1: Protein | Mass: 37058.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #2: Protein | Mass: 52938.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #3: Protein/peptide | Mass: 3201.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #4: Protein | Mass: 49416.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #5: Protein | Mass: 39057.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #8: Protein | Mass: 7118.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #9: Protein/peptide | Mass: 3902.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #10: Protein/peptide | Mass: 3699.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #11: Protein/peptide | Mass: 4147.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #12: Protein/peptide | Mass: 4071.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #13: Protein/peptide | Mass: 3157.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #17: Protein/peptide | Mass: 3510.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #19: Protein | Mass: 6466.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #20: Protein/peptide | Mass: 2531.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #21: Protein/peptide | Mass: 4881.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Cytochrome b559 subunit ... , 2 types, 2 molecules EF
| #6: Protein | Mass: 8598.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #7: Protein/peptide | Mass: 3535.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Oxygen-evolving enhancer protein ... , 3 types, 3 molecules OPQ
| #14: Protein | Mass: 25704.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #15: Protein | Mass: 20440.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #16: Protein | Mass: 16943.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 1 types, 1 molecules X
| #18: Protein/peptide | Mass: 3132.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 2 types, 4 molecules 


| #31: Sugar | | #32: Sugar | ChemComp-LMU / | |
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-Non-polymers , 13 types, 69 molecules 
























| #22: Chemical | ChemComp-OEX / | ||||||||||||||||||||
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| #23: Chemical | ChemComp-FE2 / | ||||||||||||||||||||
| #24: Chemical | | #25: Chemical | ChemComp-CLA / #26: Chemical | #27: Chemical | ChemComp-BCR / #28: Chemical | ChemComp-SQD / | #29: Chemical | ChemComp-LMG / #30: Chemical | ChemComp-LHG / #33: Chemical | ChemComp-BCT / | #34: Chemical | ChemComp-PL9 / | #35: Chemical | ChemComp-HEM / | #36: Water | ChemComp-HOH / | |
-Details
| Has ligand of interest | N |
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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: Photosystem II Intermediate / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL |
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| Molecular weight | Value: 0.4 MDa / Experimental value: YES |
| Source (natural) | Organism: ![]() |
| Buffer solution | pH: 6 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
| 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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm |
| Specimen holder | Cryogen: NITROGEN |
| Image recording | Electron dose: 46.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 24435 |
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Processing
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| CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 8293123 | ||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 361852 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
| Refine LS restraints |
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About Yorodumi





Israel, 1items
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FIELD EMISSION GUN