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Yorodumi- PDB-6kac: Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from C... -
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-Basic information
Entry | Database: PDB / ID: 6kac | ||||||||||||||||||
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Title | Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii | ||||||||||||||||||
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Keywords | PHOTOSYNTHESIS / PhotosystemII / supercomplex | ||||||||||||||||||
Function / homology | Function and homology information thylakoid light-harvesting complex / photosystem II antenna complex / nonphotochemical quenching / PSII associated light-harvesting complex II / photosystem II repair / plastoglobule / chloroplast thylakoid lumen / photosystem II assembly / photosystem II oxygen evolving complex / photosynthesis, light harvesting in photosystem I ...thylakoid light-harvesting complex / photosystem II antenna complex / nonphotochemical quenching / PSII associated light-harvesting complex II / photosystem II repair / plastoglobule / chloroplast thylakoid lumen / photosystem II assembly / photosystem II oxygen evolving complex / photosynthesis, light harvesting in photosystem I / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / response to herbicide / photosystem II / 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 / response to light stimulus / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / calcium ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||||||||
Authors | Sheng, X. / Li, A.J. / Song, D.F. / Liu, Z.F. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Nat Plants / Year: 2019 Title: Structural insight into light harvesting for photosystem II in green algae. Authors: Xin Sheng / Akimasa Watanabe / Anjie Li / Eunchul Kim / Chihong Song / Kazuyoshi Murata / Danfeng Song / Jun Minagawa / Zhenfeng Liu / Abstract: Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II ...Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II (PSII) to form various supercomplexes, including the CSML type, which is the largest PSII-LHCII supercomplex in algae and plants that is presently known. Here, we report high-resolution cryo-electron microscopy (cryo-EM) maps and structural models of the CSML and CS supercomplexes from C. reinhardtii. The CS supercomplex contains an LhcbM1-LhcbM2/7-LhcbM3 heterotrimer in the strongly associated LHCII, and the LhcbM1 subunit assembles with CP43 through two interfacial galactolipid molecules. The loosely and moderately associated LHCII trimers interact closely with the minor antenna complex CP29 to form an intricate subcomplex bound to CP47 in the CSML supercomplex. A notable direct pathway is established for energy transfer from the loosely associated LHCII to the PSII reaction centre, as well as several indirect routes. Structure-based computational analysis on the excitation energy transfer within the two supercomplexes provides detailed mechanistic insights into the light-harvesting process in green algae. | ||||||||||||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 6kac.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6kac.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6kac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kac_validation.pdf.gz | 13.8 MB | Display | wwPDB validaton report |
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Full document | 6kac_full_validation.pdf.gz | 14.8 MB | Display | |
Data in XML | 6kac_validation.xml.gz | 336.1 KB | Display | |
Data in CIF | 6kac_validation.cif.gz | 434.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/6kac ftp://data.pdbj.org/pub/pdb/validation_reports/ka/6kac | HTTPS FTP |
-Related structure data
Related structure data | 9955MC 9956C 6kadC 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
-Photosystem II ... , 14 types, 28 molecules AaBbVvCcDdHhIiJjKkLlMmTtWwZz
#1: Protein | Mass: 39066.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P07753, photosystem II #2: Protein | Mass: 56159.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P37255 #3: Protein/peptide | Mass: 3333.058 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P50370*PLUS #4: Protein | Mass: 50680.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P10898 #5: Protein | Mass: 39474.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P06007, photosystem II #8: Protein | Mass: 9445.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P22666 #9: Protein/peptide | Mass: 4245.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59763 #10: Protein/peptide | Mass: 4291.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: O19930 #11: Protein/peptide | Mass: 5062.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P18263 #12: Protein/peptide | Mass: 4431.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P32974 #13: Protein/peptide | Mass: 3762.433 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P92277 #17: Protein/peptide | Mass: 3639.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P37256 #18: Protein | Mass: 12155.054 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9SPI9 #20: Protein | Mass: 6565.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P92276 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#6: Protein | Mass: 9312.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P48268 #7: Protein/peptide | Mass: 4986.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q08363 |
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-Oxygen-evolving enhancer protein ... , 3 types, 6 molecules OoPpQq
#14: Protein | Mass: 30557.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12853 #15: Protein | Mass: 25930.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P11471 #16: Protein | Mass: 21860.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12852 |
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-Protein , 3 types, 6 molecules XxRrUu
#19: Protein | Mass: 9894.716 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I846 #23: Protein | Mass: 29970.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93WD2 #26: Protein | Mass: 19116.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I5A0 |
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-Chlorophyll a-b binding protein, ... , 4 types, 8 molecules NnGgSsYy
#21: Protein | Mass: 27405.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93WL4 #22: Protein | Mass: 26675.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93WE0 #24: Protein | Mass: 30742.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9FEK6 #25: Protein | Mass: 27591.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93VE0 |
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-Protein/peptide , 2 types, 4 molecules 1043
#27: Protein/peptide | Mass: 1738.856 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) #28: Protein/peptide | Mass: 2380.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) |
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-Sugars , 2 types, 16 molecules
#37: Sugar | ChemComp-DGD / #42: Sugar | ChemComp-LMU / |
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-Non-polymers , 17 types, 897 molecules
#29: Chemical | #30: Chemical | #31: Chemical | ChemComp-CL / #32: Chemical | ChemComp-CLA / #33: Chemical | ChemComp-PHO / #34: Chemical | ChemComp-BCR / #35: Chemical | ChemComp-SQD / #36: Chemical | ChemComp-LMG / #38: Chemical | ChemComp-LHG / #39: Chemical | #40: Chemical | #41: Chemical | #43: Chemical | ChemComp-CHL / #44: Chemical | ChemComp-LUT / ( #45: Chemical | ChemComp-XAT / ( #46: Chemical | ChemComp-NEX / ( |
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