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Yorodumi- PDB-8iwh: Structure and characteristics of a photosystem II supercomplex co... -
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-Basic information
Entry | Database: PDB / ID: 8iwh | ||||||||||||||||||||||||||||||
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Title | Structure and characteristics of a photosystem II supercomplex containing monomeric LHCX and dimeric FCPII antennae from the diatom Thalassiosira pseudonana | ||||||||||||||||||||||||||||||
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Keywords | PHOTOSYNTHESIS / PSII supercomplex / LHCX / FCP | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosystem II assembly / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / plastid ...light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosystem II assembly / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / plastid / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / response to light stimulus / photosynthesis / respiratory electron transport chain / chloroplast / electron transfer activity / oxidoreductase activity / protein stabilization / iron ion binding / calcium ion binding / heme binding / membrane / metal ion binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Thalassiosira pseudonana (Diatom) | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å | ||||||||||||||||||||||||||||||
Authors | Feng, Y. / Li, Z.H. / Wang, W.D. / Shen, J.R. | ||||||||||||||||||||||||||||||
Funding support | China, 9items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII. Authors: Yue Feng / Zhenhua Li / Xiaoyi Li / Lili Shen / Xueyang Liu / Cuicui Zhou / Jinyang Zhang / Min Sang / Guangye Han / Wenqiang Yang / Tingyun Kuang / Wenda Wang / Jian-Ren Shen / Abstract: Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We ...Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8iwh.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8iwh.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 8iwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iwh_validation.pdf.gz | 16.1 MB | Display | wwPDB validaton report |
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Full document | 8iwh_full_validation.pdf.gz | 16.8 MB | Display | |
Data in XML | 8iwh_validation.xml.gz | 332.6 KB | Display | |
Data in CIF | 8iwh_validation.cif.gz | 424.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/8iwh ftp://data.pdbj.org/pub/pdb/validation_reports/iw/8iwh | HTTPS FTP |
-Related structure data
Related structure data | 35766MC 8j0dC 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 |
-Links
-Assembly
Deposited unit |
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-Components
-Photosystem II ... , 18 types, 36 molecules AaBbCcDdGgHhIiJjKkLlMmnNTtWwXx...
#1: Protein | Mass: 36982.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0W2, photosystem II #2: Protein | Mass: 56465.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0P5 #3: Protein | Mass: 51776.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T1 #4: Protein | Mass: 39089.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T0, photosystem II #7: Protein | Mass: 18176.705 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8CC14 #8: Protein | Mass: 7391.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0P8 #9: Protein/peptide | Mass: 3940.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0U9 #10: Protein/peptide | Mass: 4045.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T9 #11: Protein/peptide | Mass: 4983.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0S8 #12: Protein/peptide | Mass: 4367.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0U0 #13: Protein | Mass: 12051.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BYH2 #14: Protein/peptide | Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Author stated that sequence was not found / Source: (natural) Thalassiosira pseudonana (Diatom) #16: Protein/peptide | Mass: 3314.011 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0P6 #19: Protein | Mass: 6096.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8C8Y3 #20: Protein/peptide | Mass: 3933.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0N4 #21: Protein | Mass: 6417.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T3 #27: Protein/peptide | Mass: 3591.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T2 #28: Protein | Mass: 22439.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BSY9 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9521.692 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0U2 #6: Protein/peptide | Mass: 4913.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0U1 |
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-Protein , 5 types, 8 molecules OoUuVv34
#15: Protein | Mass: 32168.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8C4I5 #17: Protein | Mass: 15486.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BVI4 #18: Protein | Mass: 17713.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0N2 #22: Protein | | Mass: 24100.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BUU4 #23: Protein | | Mass: 21058.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BVI1 |
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-Fucoxanthin chlorophyll a/c ... , 4 types, 8 molecules 56709281
#24: Protein | Mass: 20872.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BX92 | ||
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#25: Protein | Mass: 21402.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8CEV5 | ||
#26: Protein | Mass: 21279.365 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B5YLU3 #29: Protein | Mass: 20786.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BX93 |
-Sugars , 2 types, 17 molecules
#38: Sugar | ChemComp-DGD / #43: Sugar | ChemComp-LMU / |
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-Non-polymers , 17 types, 330 molecules
#30: Chemical | ChemComp-BCR / #31: Chemical | #32: Chemical | #33: Chemical | ChemComp-CLA / #34: Chemical | ChemComp-PHO / #35: Chemical | #36: Chemical | ChemComp-LHG / #37: Chemical | ChemComp-SQD / #39: Chemical | ChemComp-LMG / #40: Chemical | #41: Chemical | #42: Chemical | ChemComp-HEM / #44: Chemical | #45: Chemical | ChemComp-A86 / ( #46: Chemical | ChemComp-DD6 / ( #47: Chemical | ChemComp-KC2 / #48: Chemical | |
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