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Yorodumi- PDB-7oui: Structure of C2S2M2-type Photosystem supercomplex from Arabidopsi... -
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-Basic information
Entry | Database: PDB / ID: 7oui | |||||||||
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Title | Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted) | |||||||||
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Keywords | PHOTOSYNTHESIS / Oxidoreductase / Complex | |||||||||
Function / homology | Function and homology information plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / photosynthesis, light harvesting in photosystem II / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen ...plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / photosynthesis, light harvesting in photosystem II / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen / response to high light intensity / thylakoid membrane / regulation of stomatal movement / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / vacuolar transport / photosystem II assembly / photosystem II oxygen evolving complex / response to abscisic acid / photosynthesis, light harvesting in photosystem I / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / apoplast / : / thylakoid / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / poly(U) RNA binding / response to herbicide / photosystem II / plastid / chlorophyll binding / chloroplast stroma / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / response to light stimulus / photosynthetic electron transport in photosystem II / photosynthesis / chloroplast / membrane => GO:0016020 / electron transfer activity / protein stabilization / endosome / iron ion binding / protein domain specific binding / mRNA binding / heme binding / endoplasmic reticulum / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å | |||||||||
Authors | Graca, A.T. / Hall, M. / Persson, K. / Schroder, W.P. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Sci Rep / Year: 2021 Title: High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction. Authors: André T Graça / Michael Hall / Karina Persson / Wolfgang P Schröder / Abstract: In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the ...In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated MnCaO-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine, P.V. / Poon, B.K. / Read, R.J. / Sobolev, O.V. / Terwilliger, T.C. / Urzhumtsev, A. / Adams, P.D. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7oui.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7oui.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 7oui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oui_validation.pdf.gz | 15 MB | Display | wwPDB validaton report |
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Full document | 7oui_full_validation.pdf.gz | 16 MB | Display | |
Data in XML | 7oui_validation.xml.gz | 374.7 KB | Display | |
Data in CIF | 7oui_validation.cif.gz | 458.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/7oui ftp://data.pdbj.org/pub/pdb/validation_reports/ou/7oui | HTTPS FTP |
-Related structure data
Related structure data | 13078MC 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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-Components
-Protein , 4 types, 10 molecules 13572648Oo
#1: Protein | Mass: 28193.934 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q39142 #2: Protein | Mass: 26452.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q9S7M0 #3: Protein | Mass: 23198.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q9LMQ2 #15: Protein | Mass: 26594.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P23321 |
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-Photosystem II ... , 12 types, 24 molecules AaBbCcDdHhIiKkLlMmTtWwZz
#4: Protein | Mass: 38830.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P83755, photosystem II #5: Protein | Mass: 56091.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56777 #6: Protein | Mass: 50086.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56778 #7: Protein | Mass: 39444.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56761, photosystem II #10: Protein | Mass: 7575.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56780 #11: Protein/peptide | Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P62100 #12: Protein/peptide | Mass: 4239.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56782 #13: Protein/peptide | Mass: 4471.075 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P60129 #14: Protein/peptide | Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P62109 #16: Protein/peptide | Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P61839 #17: Protein | Mass: 6036.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q39194 #19: Protein | Mass: 6569.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56790 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#8: Protein | Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56779 #9: Protein/peptide | Mass: 4428.228 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P62095 |
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-Protein/peptide , 2 types, 4 molecules XxUu
#18: Protein/peptide | Mass: 4186.916 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: A0A7G2E9B1 #23: Protein/peptide | Mass: 3178.810 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q39195 |
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-Chlorophyll a-b binding protein ... , 3 types, 10 molecules SsGNYgnyRr
#20: Protein | Mass: 25232.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q9XF89 #21: Protein | Mass: 24885.072 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P04778 #22: Protein | Mass: 27302.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q07473 |
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-Sugars , 1 types, 8 molecules
#35: Sugar | ChemComp-DGD / |
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-Non-polymers , 18 types, 505 molecules
#24: Chemical | ChemComp-CHL / #25: Chemical | ChemComp-CLA / #26: Chemical | ChemComp-LHG / #27: Chemical | ChemComp-PHO / #28: Chemical | ChemComp-BCR / #29: Chemical | ChemComp-SQD / #30: Chemical | ChemComp-LMG / #31: Chemical | ChemComp-PL9 / #32: Chemical | ChemComp-AJP / #33: Chemical | #34: Chemical | #36: Chemical | ChemComp-CA / #37: Chemical | #38: Chemical | #39: Chemical | ChemComp-LUT / ( #40: Chemical | ChemComp-NEX / ( |
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