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Yorodumi- PDB-8c29: Cryo-EM structure of photosystem II C2S2 supercomplex from Norway... -
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Entry | Database: PDB / ID: 8c29 | ||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of photosystem II C2S2 supercomplex from Norway spruce (Picea abies) at 2.8 Angstrom resolution | ||||||||||||||||||||||||||||||
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Keywords | MEMBRANE PROTEIN / Membrane protein complex / Photosynthesis / Photosystem / Gymnosperm | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / 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 / photosystem I / photosynthetic electron transport chain ...photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / 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 / photosystem I / photosynthetic electron transport chain / response to herbicide / photosystem II / 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 / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Picea abies (Norway spruce) | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.785 Å | ||||||||||||||||||||||||||||||
Authors | Kopecny, D. / Semchonok, D.A. / Kouril, R. | ||||||||||||||||||||||||||||||
Funding support | Czech Republic, Germany, 9items
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Citation | Journal: Nat Plants / Year: 2023 Title: Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and α-tocopherol. Authors: Monika Opatíková / Dmitry A Semchonok / David Kopečný / Petr Ilík / Pavel Pospíšil / Iva Ilíková / Pavel Roudnický / Sanja Ćavar Zeljković / Petr Tarkowski / Fotis L Kyrilis / ...Authors: Monika Opatíková / Dmitry A Semchonok / David Kopečný / Petr Ilík / Pavel Pospíšil / Iva Ilíková / Pavel Roudnický / Sanja Ćavar Zeljković / Petr Tarkowski / Fotis L Kyrilis / Farzad Hamdi / Panagiotis L Kastritis / Roman Kouřil / Abstract: The heart of oxygenic photosynthesis is the water-splitting photosystem II (PSII), which forms supercomplexes with a variable amount of peripheral trimeric light-harvesting complexes (LHCII). Our ...The heart of oxygenic photosynthesis is the water-splitting photosystem II (PSII), which forms supercomplexes with a variable amount of peripheral trimeric light-harvesting complexes (LHCII). Our knowledge of the structure of green plant PSII supercomplex is based on findings obtained from several representatives of green algae and flowering plants; however, data from a non-flowering plant are currently missing. Here we report a cryo-electron microscopy structure of PSII supercomplex from spruce, a representative of non-flowering land plants, at 2.8 Å resolution. Compared with flowering plants, PSII supercomplex in spruce contains an additional Ycf12 subunit, Lhcb4 protein is replaced by Lhcb8, and trimeric LHCII is present as a homotrimer of Lhcb1. Unexpectedly, we have found α-tocopherol (α-Toc)/α-tocopherolquinone (α-TQ) at the boundary between the LHCII trimer and the inner antenna CP43. The molecule of α-Toc/α-TQ is located close to chlorophyll a614 of one of the Lhcb1 proteins and its chromanol/quinone head is exposed to the thylakoid lumen. The position of α-Toc in PSII supercomplex makes it an ideal candidate for the sensor of excessive light, as α-Toc can be oxidized to α-TQ by high-light-induced singlet oxygen at low lumenal pH. The molecule of α-TQ appears to shift slightly into the PSII supercomplex, which could trigger important structure-functional modifications in PSII supercomplex. Inspection of the previously reported cryo-electron microscopy maps of PSII supercomplexes indicates that α-Toc/α-TQ can be present at the same site also in PSII supercomplexes from flowering plants, but its identification in the previous studies has been hindered by insufficient resolution. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 8c29.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8c29.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8c29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c29_validation.pdf.gz | 14.3 MB | Display | wwPDB validaton report |
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Full document | 8c29_full_validation.pdf.gz | 15.3 MB | Display | |
Data in XML | 8c29_validation.xml.gz | 328.5 KB | Display | |
Data in CIF | 8c29_validation.cif.gz | 408 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/8c29 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/8c29 | HTTPS FTP |
-Related structure data
Related structure data | 16389MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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-Assembly
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-Components
-Photosystem II ... , 14 types, 28 molecules AaBbCcDdHhIiKkLlMmTtUuVvXxZz
#1: Protein | Mass: 38803.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbA / Source: (natural) Picea abies (Norway spruce) / References: UniProt: P50155, photosystem II #2: Protein | Mass: 56375.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbB / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGX1 #3: Protein | Mass: 51785.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbC / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGZ0 #4: Protein | Mass: 39483.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbD / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGX6, photosystem II #8: Protein | Mass: 7941.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbH / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGS7 #9: Protein/peptide | Mass: 4184.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbI / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGS4 #10: Protein | Mass: 6804.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbK / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGX8 #11: Protein/peptide | Mass: 4475.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbL / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGV2 #12: Protein/peptide | Mass: 3952.636 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbM / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A2CHR7 #16: Protein/peptide | Mass: 3962.781 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbTc / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGU2 #17: Protein | Mass: 14189.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbTn / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NJW3 #18: Protein/peptide | Mass: 3490.290 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Psb30 / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGY5 #20: Protein | Mass: 12956.940 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbX / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NTS2 #21: Protein | Mass: 6412.558 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbZ / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGT1 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9478.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbE / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGW6 #6: Protein/peptide | Mass: 4476.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbF / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGT7 |
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-Chlorophyll a-b binding protein, ... , 3 types, 10 molecules GNYgnyRrSs
#7: Protein | Mass: 29112.004 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: Lhcb1 / Source: (natural) Picea abies (Norway spruce) / References: UniProt: Q40771 #14: Protein | Mass: 32767.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Lhcb4.3 / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NKX0 #15: Protein | Mass: 32287.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CP26 / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NKM0 |
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-Protein , 2 types, 4 molecules OoWw
#13: Protein | Mass: 36089.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbO / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NRV4 #19: Protein | Mass: 15266.507 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbW / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NLC2 |
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-Sugars , 1 types, 4 molecules
#33: Sugar | ChemComp-DGD / |
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