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Open data
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Basic information
Entry | Database: PDB / ID: 7ymi | ||||||||||||
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Title | PSII-Pcb Dimer of Acaryochloris Marina | ||||||||||||
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![]() | PHOTOSYNTHESIS / Photosystem II / Pcb | ||||||||||||
Function / homology | ![]() photosystem / 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 / plasma membrane-derived thylakoid membrane ...photosystem / 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 / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / manganese ion binding / 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: 3.3 Å | ||||||||||||
![]() | Shen, L.L. / Gao, Y.Z. / Wang, W.D. / Zhang, X. / Shen, J.R. / Wang, P.Y. / Han, G.Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a large photosystem II supercomplex from Acaryochloris marina. Authors: Shen, L.L. / Gao, Y.Z. / Wang, W.D. / Zhang, X. / Shen, J.R. / Wang, P.Y. / Han, G.Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 14.4 MB | Display | ![]() |
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Full document | ![]() | 15.4 MB | Display | |
Data in XML | ![]() | 334.9 KB | Display | |
Data in CIF | ![]() | 421 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33929MC ![]() 7ymmC 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 ... , 14 types, 28 molecules AaBbCcDdFfHhIiKkLlMmTtXxYyZz
#1: Protein | Mass: 39695.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 56518.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 53978.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 39291.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 11277.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 7683.901 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein/peptide | Mass: 3948.692 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein/peptide | Mass: 4939.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein/peptide | Mass: 4254.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein/peptide | Mass: 3614.302 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein/peptide | Mass: 5442.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein/peptide | Mass: 4443.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein/peptide | Mass: 4015.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | Mass: 6395.632 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-High light inducible ... , 4 types, 8 molecules 26153748
#16: Protein | Mass: 38753.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | Mass: 38612.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | Mass: 38707.781 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #20: Protein | Mass: 37967.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein / Protein/peptide / Sugars , 3 types, 8 molecules EeGg![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#17: Protein/peptide | Mass: 3507.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #27: Sugar | ChemComp-DGD / #5: Protein | Mass: 9495.788 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 11 types, 308 molecules ![](data/chem/img/CL7.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/8CT.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/ZEX.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/8CT.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/ZEX.gif)
#21: Chemical | ChemComp-CL7 / #22: Chemical | ChemComp-PHO / #23: Chemical | ChemComp-8CT / ( #24: Chemical | ChemComp-SQD / #25: Chemical | ChemComp-LHG / #26: Chemical | ChemComp-LMG / #28: Chemical | #29: Chemical | #30: Chemical | #31: Chemical | #32: Chemical | ChemComp-ZEX / ( |
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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: PSII-Pcb Dimer of Acaryochloris Marina / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL |
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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: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132346 / Symmetry type: POINT |