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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9776 | |||||||||
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Title | Structure of C2S1M1-type PSII-FCPII supercomplex from diatom | |||||||||
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Function / homology | ![]() photosystem II assembly / photosystem II oxygen evolving complex / photosystem II stabilization / thylakoid / photosystem II / extrinsic component of membrane / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis ...photosystem II assembly / photosystem II oxygen evolving complex / photosystem II stabilization / thylakoid / photosystem II / extrinsic component of membrane / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Nagao R / Kato K / Shen JR / Miyazaki N / Akita F | |||||||||
![]() | ![]() 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. | |||||||||
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 30 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 43.7 KB 43.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 81.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 358.4 KB | Display | ![]() |
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Full document | ![]() | 357.9 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j3zMC ![]() 9775C ![]() 9777C ![]() 6j3yC ![]() 6j40C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : C2S1M1-type PSII-FCPII supercomplex
+Supramolecule #1: C2S1M1-type PSII-FCPII supercomplex
+Macromolecule #1: Photosystem II reaction center protein D1
+Macromolecule #2: Photosystem II chlorophyll protein CP47
+Macromolecule #3: Photosystem II chlorophyll protein CP43
+Macromolecule #4: Photosystem II reaction center protein D2
+Macromolecule #5: Cytochrome b559 subunit alpha
+Macromolecule #6: Cytochrome b559 subunit beta
+Macromolecule #7: Photosystem II reaction center protein H
+Macromolecule #8: Photosystem II reaction center protein I
+Macromolecule #9: Photosystem II reaction center protein J
+Macromolecule #10: Photosystem II reaction center protein K
+Macromolecule #11: Photosystem II reaction center protein L
+Macromolecule #12: Photosystem II reaction center protein M
+Macromolecule #13: Extrinsic protein in photosystem II
+Macromolecule #14: Photosystem II reaction center protein T
+Macromolecule #15: Extrinsic protein in photosystem II
+Macromolecule #16: Cytochrome c-550
+Macromolecule #17: Photosystem II reaction center protein Ycf12
+Macromolecule #18: Photosystem II reaction center X protein
+Macromolecule #19: Photosystem II reaction center protein Z
+Macromolecule #20: Extrinsic protein in photosystem II
+Macromolecule #21: Photosystem II reaction center protein W
+Macromolecule #22: Unknown protein 0
+Macromolecule #23: Unknown protein 1
+Macromolecule #24: Unknown protein 2
+Macromolecule #25: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
+Macromolecule #26: Fucoxanthin chlorophyll a/c-binding protein monomer 1
+Macromolecule #27: Fucoxanthin chlorophyll a/c-binding protein monomer 2
+Macromolecule #28: Fucoxanthin chlorophyll a/c-binding protein monomer 3
+Macromolecule #29: FE (II) ION
+Macromolecule #30: CHLOROPHYLL A
+Macromolecule #31: PHEOPHYTIN A
+Macromolecule #32: BETA-CAROTENE
+Macromolecule #33: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #34: BICARBONATE ION
+Macromolecule #35: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #36: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #37: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #38: CA-MN4-O5 CLUSTER
+Macromolecule #39: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #40: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #41: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #42: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.256 mg/mL | ||||||
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Buffer | pH: 6.5 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |