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Yorodumi- PDB-7czl: Structural insights into a dimeric Psb27-photosystem II complex f... -
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-Basic information
Entry | Database: PDB / ID: 7czl | ||||||
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Title | Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus | ||||||
Components |
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Keywords | PLANT PROTEIN / dimeric photosystem II (PSII)-Psb27 complex from a cyanobacterium Thermosynechococcus vulcanus | ||||||
Function / homology | Function and homology information photosystem II stabilization / oxygen evolving activity / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding ...photosystem II stabilization / oxygen evolving activity / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å | ||||||
Authors | Pi, X. / Huang, G. / Xiao, Y. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium . Authors: Guoqiang Huang / Yanan Xiao / Xiong Pi / Liang Zhao / 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 catalyzes light-driven water oxidation, leading to the conversion of light energy into chemical energy and the release of molecular ...Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyzes light-driven water oxidation, leading to the conversion of light energy into chemical energy and the release of molecular oxygen. Psb27 is a small thylakoid lumen-localized protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex. The exact location and binding fashion of Psb27 in the intermediate PSII remain elusive. Here, we report the structure of a dimeric Psb27-PSII complex purified from a deletion mutant (ΔPsbV) of the cyanobacterium , solved by cryo-electron microscopy. Our structure showed that Psb27 is associated with CP43 at the luminal side, with specific interactions formed between Helix 2 and Helix 3 of Psb27 and a loop region between Helix 3 and Helix 4 of CP43 (loop C) as well as the large, lumen-exposed and hydrophilic E-loop of CP43. The binding of Psb27 imposes some conflicts with the N-terminal region of PsbO and also induces some conformational changes in CP43, CP47, and D2. This makes PsbO unable to bind in the Psb27-PSII. Conformational changes also occurred in D1, PsbE, PsbF, and PsbZ; this, together with the conformational changes occurred in CP43, CP47, and D2, may prevent the binding of PsbU and induce dissociation of PsbJ. This structural information provides important insights into the regulation mechanism of Psb27 in the biogenesis and repair of PSII. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 7czl.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7czl.ent.gz | 923.3 KB | Display | PDB format |
PDBx/mmJSON format | 7czl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/7czl ftp://data.pdbj.org/pub/pdb/validation_reports/cz/7czl | HTTPS FTP |
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-Related structure data
Related structure data | 30511MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosystem II ... , 13 types, 26 molecules AaBbCcDdHhIiKkLlMmTtZzYyXx
#1: Protein | Mass: 35894.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P51765, photosystem II #2: Protein | Mass: 56096.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR1 #3: Protein | Mass: 48648.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR7 #4: Protein | Mass: 38005.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR8, photosystem II #7: Protein | Mass: 6986.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19052 #8: Protein/peptide | Mass: 3923.706 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12240 #9: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19054 #10: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12241 #11: Protein/peptide | Mass: 3678.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12312 #12: Protein/peptide | Mass: 3620.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12313 #13: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR5 #14: Protein/peptide | Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR3 #16: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR4 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 7495.497 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12238 #6: Protein/peptide | Mass: 3461.166 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12239 |
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-Protein , 1 types, 2 molecules nN
#15: Protein | Mass: 12234.814 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) |
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-Sugars , 2 types, 14 molecules
#22: Sugar | ChemComp-LMT / #26: Sugar | ChemComp-DGD / |
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-Non-polymers , 12 types, 132 molecules
#17: Chemical | ChemComp-CLA / #18: Chemical | ChemComp-PHO / #19: Chemical | ChemComp-PQ9 / #20: Chemical | ChemComp-BCR / #21: Chemical | #23: Chemical | ChemComp-SQD / #24: Chemical | #25: Chemical | ChemComp-MGE / ( #27: Chemical | #28: Chemical | #29: Chemical | #30: Chemical | |
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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 |
-Sample preparation
Component | Name: PSII-Psb27 / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL |
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Source (natural) | Organism: Thermosynechococcus vulcanus (bacteria) |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87473 / Symmetry type: POINT | ||||||||||||||||||||||||
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