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Open data
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Basic information
Entry | Database: PDB / ID: 7dxh | |||||||||
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Title | Cryo-EM structure of PSII intermediate Psb28-PSII complex | |||||||||
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![]() | PLANT PROTEIN / Photosystem II / Cryo-EM / assembly / repair / Psb28 / Tsl0063 | |||||||||
Function / homology | ![]() photosystem II oxygen evolving complex / 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 II oxygen evolving complex / 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 / 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: 3.14 Å | |||||||||
![]() | Sui, S.F. / Shen, J.R. / Han, G.Y. / Xiao, Y.N. / Huang, G.Q. | |||||||||
![]() | ![]() Title: Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063. Authors: Yanan Xiao / Guoqiang Huang / Xin You / Qingjun Zhu / Wenda Wang / Tingyun Kuang / Guangye Han / Sen-Fang Sui / Jian-Ren Shen / ![]() ![]() Abstract: Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. ...Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. We analysed the structures of two Psb28-bound PSII intermediates, Psb28-RC47 and Psb28-PSII, purified from a psbV-deletion strain of the thermophilic cyanobacterium Thermosynechococcus vulcanus, using cryo-electron microscopy. Both Psb28-RC47 and Psb28-PSII bind one Psb28, one Tsl0063 and an unknown subunit. Psb28 is located at the cytoplasmic surface of PSII and interacts with D1, D2 and CP47, whereas Tsl0063 is a transmembrane subunit and binds at the side of CP47/PsbH. Substantial structural perturbations are observed at the acceptor side, which result in conformational changes of the quinone (Q) and non-haem iron binding sites and thus may protect PSII from photodamage during assembly. These results provide a solid structural basis for understanding the assembly process of native PSII. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 475.7 KB | Display | ![]() |
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PDB format | ![]() | 390.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 92.1 KB | Display | |
Data in CIF | ![]() | 120.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30909MC ![]() 7dxaC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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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, 14 molecules Aabdhilmtxckzy
#1: Protein | Mass: 13188.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein | Mass: 39792.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 56068.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 38404.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 7227.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein/peptide | Mass: 4015.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein/peptide | Mass: 3878.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 49207.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein/peptide | Mass: 5028.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#16: Protein | Mass: 6766.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein/peptide | Mass: 3228.035 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: 9580.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#7: Protein/peptide | Mass: 5067.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein / Protein/peptide , 2 types, 2 molecules BC
#18: Protein/peptide | Mass: 1652.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 5943.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 3 types, 8 molecules ![](data/chem/img/DGD.gif)
![](data/chem/img/LMT.gif)
![](data/chem/img/HTG.gif)
![](data/chem/img/LMT.gif)
![](data/chem/img/HTG.gif)
#24: Sugar | ChemComp-DGD / #26: Sugar | #31: Sugar | ChemComp-HTG / | |
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-Non-polymers , 10 types, 61 molecules ![](data/chem/img/MGE.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/PQ9.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/PQ9.gif)
![](data/chem/img/HEM.gif)
#19: Chemical | ChemComp-MGE / ( #20: Chemical | #21: Chemical | ChemComp-CLA / #22: Chemical | ChemComp-BCR / #23: Chemical | #25: Chemical | #27: Chemical | ChemComp-FE2 / | #28: Chemical | ChemComp-PQ9 / | #29: Chemical | Mass: 294.408 Da / Num. of mol.: 2 / Source method: obtained synthetically #30: Chemical | ChemComp-HEM / | |
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-Details
Has ligand of interest | N |
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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 structure of PSII intermediate Psb28-PSII complex. Type: COMPLEX / Entity ID: #1-#11, #13-#18 / 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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194738 / Symmetry type: POINT | ||||||||||||||||||||||||
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