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Yorodumi- EMDB-30012: Organization and energy transfer in a huge diatom PSI-FCPI superc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30012 | |||||||||
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Title | Organization and energy transfer in a huge diatom PSI-FCPI supercomplex | |||||||||
Map data | diatom PSI-FCPI | |||||||||
Sample |
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Function / homology | Function and homology information light-harvesting complex / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / : / photosystem I reaction center / photosystem I / photosystem I / plastid / photosynthetic electron transport in photosystem I ...light-harvesting complex / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / : / photosystem I reaction center / photosystem I / photosystem I / plastid / photosynthetic electron transport in photosystem I / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / oxidoreductase activity / identical protein binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Chaetoceros gracilis (Diatom) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.38 Å | |||||||||
Authors | Xiong P / Caizhe X | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex. Authors: Caizhe Xu / Xiong Pi / Yawen Huang / Guangye Han / Xiaobo Chen / Xiaochun Qin / Guoqiang Huang / Songhao Zhao / Yanyan Yang / Tingyun Kuang / Wenda Wang / Sen-Fang Sui / Jian-Ren Shen / Abstract: Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of ...Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of fucoxanthin-chlorophyll a/c proteins (FCPIs). We report the structure of PSI-FCPI from a diatom Chaetoceros gracilis at 2.38 Å resolution by single-particle cryo-electron microscopy. PSI-FCPI is a monomeric supercomplex consisting of 12 core and 24 antenna subunits (FCPIs), and 326 chlorophylls a, 34 chlorophylls c, 102 fucoxanthins, 35 diadinoxanthins, 18 β-carotenes and some electron transfer cofactors. Two subunits designated PsaR and PsaS were found in the core, whereas several subunits were lost. The large number of pigments constitute a unique and huge network ensuring efficient energy harvesting, transfer and dissipation. These results provide a firm structural basis for unraveling the mechanisms of light-energy harvesting, transfer and quenching in the diatom PSI-FCPI, and also important clues to evolutionary changes of PSI-LHCI. | |||||||||
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_30012.map.gz | 500.7 MB | EMDB map data format | |
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Header (meta data) | emd-30012-v30.xml emd-30012.xml | 44.9 KB 44.9 KB | Display Display | EMDB header |
Images | emd_30012.png | 146.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30012 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30012 | HTTPS FTP |
-Validation report
Summary document | emd_30012_validation.pdf.gz | 521.7 KB | Display | EMDB validaton report |
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Full document | emd_30012_full_validation.pdf.gz | 521.2 KB | Display | |
Data in XML | emd_30012_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_30012_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30012 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30012 | HTTPS FTP |
-Related structure data
Related structure data | 6ly5MC 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_30012.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | diatom PSI-FCPI | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : a huge diatom PSI-FCPI supercomplex
+Supramolecule #1: a huge diatom PSI-FCPI supercomplex
+Macromolecule #1: FCPI-7
+Macromolecule #2: FCPI-1
+Macromolecule #3: FCPI-11
+Macromolecule #4: FCPI-6
+Macromolecule #5: FCPI-5
+Macromolecule #6: FCPI-8
+Macromolecule #7: FCPI-4
+Macromolecule #8: FCPI-10
+Macromolecule #9: FCPI-3
+Macromolecule #10: FCPI-9
+Macromolecule #11: FCPI-13
+Macromolecule #12: FCPI-14
+Macromolecule #13: FCPI-16
+Macromolecule #14: FCPI-21
+Macromolecule #15: FCPI
+Macromolecule #16: FCPI-24
+Macromolecule #17: FCPI-23
+Macromolecule #18: FCPI-12
+Macromolecule #19: FCPI-17
+Macromolecule #20: PsaA
+Macromolecule #21: PsaB
+Macromolecule #22: PsaC
+Macromolecule #23: PsaD
+Macromolecule #24: PsaE
+Macromolecule #25: PsaF
+Macromolecule #26: PsaI
+Macromolecule #27: PsaJ
+Macromolecule #28: PsaL
+Macromolecule #29: PsaM
+Macromolecule #30: PsaS
+Macromolecule #31: PsaR
+Macromolecule #32: FCPI-2
+Macromolecule #33: FCPI-19
+Macromolecule #34: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...
+Macromolecule #35: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
+Macromolecule #36: CHLOROPHYLL A
+Macromolecule #37: Chlorophyll c1
+Macromolecule #38: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #39: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #40: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #41: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #42: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #43: PHYLLOQUINONE
+Macromolecule #44: BETA-CAROTENE
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |