+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10798 | |||||||||
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Title | Plant PSI-ferredoxin-plastocyanin supercomplex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Membrane complex / photosystem I / ferredoxin / light harvesting / excitation transfer / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information plastoglobule / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / photosynthetic electron transport in photosystem I / chlorophyll binding ...plastoglobule / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / photosynthetic electron transport in photosystem I / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / copper ion binding / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Pisum sativum (garden pea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Caspy I / Nelson N | |||||||||
Funding support | Israel, 2 items
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Citation | Journal: Nat Plants / Year: 2020 Title: The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin. Authors: Ido Caspy / Anna Borovikova-Sheinker / Daniel Klaiman / Yoel Shkolnisky / Nathan Nelson / Abstract: The ability of photosynthetic organisms to use sunlight as a sole source of energy is endowed by two large membrane complexes-photosystem I (PSI) and photosystem II (PSII). PSI and PSII are the ...The ability of photosynthetic organisms to use sunlight as a sole source of energy is endowed by two large membrane complexes-photosystem I (PSI) and photosystem II (PSII). PSI and PSII are the fundamental components of oxygenic photosynthesis, providing oxygen, food and an energy source for most living organisms on Earth. Currently, high-resolution crystal structures of these complexes from various organisms are available. The crystal structures of megadalton complexes have revealed excitation transfer and electron-transport pathways within the various complexes. PSI is defined as plastocyanin-ferredoxin oxidoreductase but a high-resolution structure of the entire triple supercomplex is not available. Here, using a new cryo-electron microscopy technique, we solve the structure of native plant PSI in complex with its electron donor plastocyanin and the electron acceptor ferredoxin. We reveal all of the contact sites and the modes of interaction between the interacting electron carriers and PSI. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10798.map.gz | 94.6 MB | EMDB map data format | |
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Header (meta data) | emd-10798-v30.xml emd-10798.xml | 38.7 KB 38.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10798_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_10798.png | 119.4 KB | ||
Filedesc metadata | emd-10798.cif.gz | 9.3 KB | ||
Others | emd_10798_half_map_1.map.gz emd_10798_half_map_2.map.gz | 80.6 MB 80.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10798 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10798 | HTTPS FTP |
-Validation report
Summary document | emd_10798_validation.pdf.gz | 901.2 KB | Display | EMDB validaton report |
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Full document | emd_10798_full_validation.pdf.gz | 900.8 KB | Display | |
Data in XML | emd_10798_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_10798_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10798 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10798 | HTTPS FTP |
-Related structure data
Related structure data | 6yezMC 6yacC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10798.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_10798_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10798_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Triple complex of photosystem I bound to ferredoxin and plastocyanin
+Supramolecule #1: Triple complex of photosystem I bound to ferredoxin and plastocyanin
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #3: Photosystem I iron-sulfur center
+Macromolecule #4: PsaD
+Macromolecule #5: PsaE
+Macromolecule #6: PsaF
+Macromolecule #7: PsaG
+Macromolecule #8: PsaH
+Macromolecule #9: Photosystem I reaction center subunit VIII
+Macromolecule #10: PsaJ
+Macromolecule #11: Photosystem I reaction center subunit X psaK
+Macromolecule #12: PsaL
+Macromolecule #13: Lhca1
+Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #15: Chlorophyll a-b binding protein 3, chloroplastic
+Macromolecule #16: Chlorophyll a-b binding protein P4, chloroplastic
+Macromolecule #17: Ferredoxin-1, chloroplastic
+Macromolecule #18: Plastocyanin, chloroplastic
+Macromolecule #19: CHLOROPHYLL A ISOMER
+Macromolecule #20: CHLOROPHYLL A
+Macromolecule #21: PHYLLOQUINONE
+Macromolecule #22: BETA-CAROTENE
+Macromolecule #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #24: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #25: IRON/SULFUR CLUSTER
+Macromolecule #26: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #27: CALCIUM ION
+Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #29: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #30: CHLOROPHYLL B
+Macromolecule #31: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #32: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
+Macromolecule #33: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...
+Macromolecule #34: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #35: COPPER (II) ION
+Macromolecule #36: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 11622 / Average exposure time: 1.4 sec. / Average electron dose: 47.05 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |