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- PDB-8zee: Cryo-EM structure of an intermediate-state PSII-PRF2' complex dur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8zee | ||||||||||||
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Title | Cryo-EM structure of an intermediate-state PSII-PRF2' complex during the process of photosystem II repair | ||||||||||||
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![]() | PHOTOSYNTHESIS | ||||||||||||
Function / homology | ![]() 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 ...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 / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
![]() | Li, A. / Liu, Z. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii Authors: Li, A. / You, T. / Pang, X. / Wang, Y. / Tian, L. / Li, X. / Liu, Z. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 464.6 KB | Display | ![]() |
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PDB format | ![]() | 385.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.9 MB | Display | ![]() |
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Full document | ![]() | 4 MB | Display | |
Data in XML | ![]() | 93 KB | Display | |
Data in CIF | ![]() | 125 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 60026MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Photosystem II ... , 12 types, 12 molecules BDHIKLMTVZCA
#1: Protein | Mass: 56089.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 39474.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 9445.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein/peptide | Mass: 4245.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein/peptide | Mass: 5062.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein/peptide | Mass: 4431.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein/peptide | Mass: 3762.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein/peptide | Mass: 3639.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein/peptide | Mass: 3333.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 6565.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 50680.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 36515.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
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#4: Protein/peptide | Mass: 4986.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules X1
#12: Protein | Mass: 9894.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#16: Protein | Mass: 10153.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 1 types, 3 molecules ![](data/chem/img/DGD.gif)
#26: Sugar |
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-Non-polymers , 11 types, 67 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/VTQ.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/VTQ.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/FE2.gif)
#17: Chemical | ChemComp-CLA / #18: Chemical | ChemComp-BCR / #19: Chemical | ChemComp-LMG / #20: Chemical | ChemComp-LHG / #21: Chemical | ChemComp-BCT / | #22: Chemical | ChemComp-PL9 / | #23: Chemical | #24: Chemical | ChemComp-HEM / | #25: Chemical | ChemComp-VTQ / | #27: Chemical | ChemComp-SQD / | #28: 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 |
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Sample preparation
Component | Name: Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6.5 |
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: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
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 K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159928 / Symmetry type: POINT |