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- PDB-8bd3: Cryo-EM structure of the Photosystem II - LHCII supercomplex from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bd3 | ||||||
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Title | Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi | ||||||
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![]() | PHOTOSYNTHESIS / Green alga / PSII / C.ohadi / membrane protein / Cryo-EM | ||||||
Function / homology | ![]() diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / photosynthesis, light harvesting / photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / protein kinase C-activating G protein-coupled receptor signaling pathway ...diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / photosynthesis, light harvesting / photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / protein kinase C-activating G protein-coupled receptor signaling pathway / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / response to herbicide / photosystem II / plastid / extrinsic component of membrane / 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 / chloroplast / electron transfer activity / protein stabilization / iron ion binding / calcium ion binding / heme binding / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å | ||||||
![]() | Fadeeva, M. / Klaiman, D. / Caspy, I. / Nelson, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Photosystem II Reveals Protective Mechanisms against Environmental Stress. Authors: Maria Fadeeva / Daniel Klaiman / Ido Caspy / Nathan Nelson / ![]() Abstract: Green alga is known for its ability to carry out photosynthesis under harsh conditions. Using cryogenic electron microscopy (cryoEM), we obtained a high-resolution structure of PSII at 2.72 Å. This ...Green alga is known for its ability to carry out photosynthesis under harsh conditions. Using cryogenic electron microscopy (cryoEM), we obtained a high-resolution structure of PSII at 2.72 Å. This structure revealed 64 subunits, which encompassed 386 chlorophylls, 86 carotenoids, four plastoquinones, and several structural lipids. At the luminal side of PSII, a unique subunit arrangement was observed to protect the oxygen-evolving complex. This arrangement involved PsbO (OEE1), PsbP (OEE2), PsbB, and PsbU (a homolog of plant OEE3). PsbU interacted with PsbO, PsbC, and PsbP, thereby stabilizing the shield of the oxygen-evolving complex. Significant changes were also observed at the stromal electron acceptor side. PsbY, identified as a transmembrane helix, was situated alongside PsbF and PsbE, which enclosed cytochrome . Supported by the adjacent C-terminal helix of Psb10, these four transmembrane helices formed a bundle that shielded cytochrome from the surrounding solvent. Moreover, the bulk of Psb10 formed a protective cap, which safeguarded the quinone site and likely contributed to the stacking of PSII complexes. Based on our findings, we propose a protective mechanism that prevents Q (plastoquinone B) from becoming fully reduced. This mechanism offers insights into the regulation of electron transfer within PSII. | ||||||
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-Validation report
Summary document | ![]() | 28.9 MB | Display | ![]() |
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Full document | ![]() | 30.6 MB | Display | |
Data in XML | ![]() | 584.6 KB | Display | |
Data in CIF | ![]() | 715 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15973MC 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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Assembly
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Components
+Chlorophyll a-b binding protein, ... , 2 types, 8 molecules 1724G9qg
+Chlorophyll a-b binding of ... , 2 types, 8 molecules 35N8pn60
+Photosystem II ... , 16 types, 32 molecules AaBbCcDdHhIiJjKkLlMmTtVvWwXxZzF1f1
+Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
+Chloroplast oxygen-evolving enhancer protein ... , 2 types, 4 molecules OoUu
+Chlorophyll a ... , 2 types, 4 molecules RrSs
+Protein , 2 types, 4 molecules YyP1p1
+Protein/peptide , 1 types, 2 molecules Q1q1
+Sugars , 2 types, 12 molecules ![](data/chem/img/DGD.gif)
![](data/chem/img/LMU.gif)
![](data/chem/img/LMU.gif)
+Non-polymers , 18 types, 884 molecules ![](data/chem/img/CHL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/NEX.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/NEX.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)