+Open data
-Basic information
Entry | Database: PDB / ID: 6j3y | ||||||
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Title | Structure of C2S2-type PSII-FCPII supercomplex from diatom | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Photosystem | ||||||
Function / homology | Function and homology information photosystem II assembly / photosystem II stabilization / thylakoid / photosystem II / extrinsic component of membrane / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / respiratory electron transport chain ...photosystem II assembly / photosystem II stabilization / thylakoid / photosystem II / extrinsic component of membrane / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / respiratory electron transport chain / protein stabilization / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Chaetoceros gracilis (Diatom) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Nagao, R. / Kato, K. / Shen, J.R. / Miyazaki, N. / Akita, F. | ||||||
Citation | Journal: Nat Plants / Year: 2019 Title: Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex. Authors: Ryo Nagao / Koji Kato / Takehiro Suzuki / Kentaro Ifuku / Ikuo Uchiyama / Yasuhiro Kashino / Naoshi Dohmae / Seiji Akimoto / Jian-Ren Shen / Naoyuki Miyazaki / Fusamichi Akita / Abstract: Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. ...Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red- and green-lineage oxyphototrophs during evolution. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6j3y.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6j3y.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6j3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j3y_validation.pdf.gz | 12.2 MB | Display | wwPDB validaton report |
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Full document | 6j3y_full_validation.pdf.gz | 13.1 MB | Display | |
Data in XML | 6j3y_validation.xml.gz | 332.7 KB | Display | |
Data in CIF | 6j3y_validation.cif.gz | 403.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/6j3y ftp://data.pdbj.org/pub/pdb/validation_reports/j3/6j3y | HTTPS FTP |
-Related structure data
Related structure data | 9775MC 9776C 9777C 6j3zC 6j40C 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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1 |
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-Components
-Photosystem II reaction center protein ... , 12 types, 24 molecules AaDdHhIiJjKkLlMmTtYyZzWw
#1: Protein | Mass: 38183.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #4: Protein | Mass: 39069.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #7: Protein | Mass: 7418.827 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B7XBY7 #8: Protein/peptide | Mass: 4427.212 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #9: Protein/peptide | Mass: 4093.833 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #10: Protein/peptide | Mass: 4978.028 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #11: Protein/peptide | Mass: 4367.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #12: Protein | Mass: 14180.403 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #14: Protein/peptide | Mass: 3711.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #17: Protein/peptide | Mass: 3609.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #19: Protein | Mass: 6528.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #21: Protein | Mass: 7848.743 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
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-Photosystem II chlorophyll protein ... , 2 types, 4 molecules BbCc
#2: Protein | Mass: 56475.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #3: Protein | Mass: 51947.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9507.667 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #6: Protein/peptide | Mass: 4912.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
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-Extrinsic protein in photosystem ... , 3 types, 6 molecules OoUuQq
#13: Protein | Mass: 26762.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE8 #15: Protein | Mass: 10137.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF0 #20: Protein | Mass: 17088.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE9 |
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-Protein , 2 types, 10 molecules Vv1112131431323334
#16: Protein | Mass: 14893.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF4 #25: Protein | Mass: 22098.182 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
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-Protein/peptide , 1 types, 2 molecules Xx
#18: Protein/peptide | Mass: 3859.647 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF2 |
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-Unknown protein ... , 3 types, 6 molecules 051627
#22: Protein/peptide | Mass: 2656.265 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #23: Protein/peptide | Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #24: Protein/peptide | Mass: 869.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
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-Sugars , 2 types, 10 molecules
#35: Sugar | ChemComp-DGD / #39: Sugar | |
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-Non-polymers , 12 types, 276 molecules
#26: Chemical | #27: Chemical | ChemComp-CLA / #28: Chemical | ChemComp-PHO / #29: Chemical | ChemComp-BCR / #30: Chemical | ChemComp-SQD / #31: Chemical | #32: Chemical | ChemComp-LHG / #33: Chemical | ChemComp-LMG / #34: Chemical | #36: Chemical | ChemComp-PL9 / #37: Chemical | ChemComp-HEM / #38: Chemical | ChemComp-A86 / ( |
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-Details
Sequence details | Unknown protein 0/1/2 are supposed to be new components of photosystem II. Sequence of the entities ...Unknown protein 0/1/2 are supposed to be new components of photosystem II. Sequence of the entities could not be assigned. |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: C2S2-type PSII-FCPII supercomplex / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL | ||||||||||||
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Molecular weight | Value: 0.85 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Chaetoceros gracilis (Diatom) | ||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.256 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: (1.14_3260: phenix.real_space_refine) / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214939 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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