- EMDB-31062: Structure of monomeric photosystem II -
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Basic information
Entry
Database: EMDB / ID: EMD-31062
Title
Structure of monomeric photosystem II
Map data
Sample
Complex: Photosystem II
Protein or peptide: x 19 types
Protein or peptide: x 1 types
Ligand: x 16 types
Function / homology
Function and homology information
photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / 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 ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / 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 / extrinsic component of membrane / 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 / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily Similarity search - Domain/homology
Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein V / Photosystem II reaction center protein Y / Cytochrome b559 subunit alpha ...Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein V / Photosystem II reaction center protein Y / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 / Photosystem II extrinsic protein U / Photosystem II reaction center protein J Similarity search - Component
Biological species
Thermosynechococcus vulcanus (bacteria)
Method
single particle reconstruction / cryo EM / Resolution: 2.78 Å
Japan Agency for Medical Research and Development (AMED)
JP18am0101072
Japan
Citation
Journal: Biochim Biophys Acta Bioenerg / Year: 2021 Title: Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer. Authors: Huaxin Yu / Tasuku Hamaguchi / Yoshiki Nakajima / Koji Kato / Keisuke Kawakami / Fusamichi Akita / Koji Yonekura / Jian-Ren Shen / Abstract: Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The ...Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.
History
Deposition
Mar 15, 2021
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Header (metadata) release
Jul 7, 2021
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Map release
Jul 7, 2021
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Update
Aug 4, 2021
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Current status
Aug 4, 2021
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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