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Yorodumi- EMDB-21320: Trimeric Photosystem I from the High-Light Tolerant Cyanobacteria... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21320 | |||||||||
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Title | Trimeric Photosystem I from the High-Light Tolerant Cyanobacteria Cyanobacterium Aponinum | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information : / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / membrane => GO:0016020 / 4 iron, 4 sulfur cluster binding ...: / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / membrane => GO:0016020 / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Cyanobacterium aponinum 0216 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Dobson Z / Toporik H / Vaughn N / Lin S / Williams D / Fromme P / Mazor Y | |||||||||
Citation | Journal: Elife / Year: 2021 Title: The structure of photosystem I from a high-light-tolerant cyanobacteria. Authors: Zachary Dobson / Safa Ahad / Jackson Vanlandingham / Hila Toporik / Natalie Vaughn / Michael Vaughn / Dewight Williams / Michael Reppert / Petra Fromme / Yuval Mazor / Abstract: Photosynthetic organisms have adapted to survive a myriad of extreme environments from the earth's deserts to its poles, yet the proteins that carry out the light reactions of photosynthesis are ...Photosynthetic organisms have adapted to survive a myriad of extreme environments from the earth's deserts to its poles, yet the proteins that carry out the light reactions of photosynthesis are highly conserved from the cyanobacteria to modern day crops. To investigate adaptations of the photosynthetic machinery in cyanobacteria to excessive light stress, we isolated a new strain of cyanobacteria, 0216, from the extreme light environment of the Sonoran Desert. Here we report the biochemical characterization and the 2.7 Å resolution structure of trimeric photosystem I from this high-light-tolerant cyanobacterium. The structure shows a new conformation of the PsaL C-terminus that supports trimer formation of cyanobacterial photosystem I. The spectroscopic analysis of this photosystem I revealed a decrease in far-red absorption, which is attributed to a decrease in the number of long- wavelength chlorophylls. Using these findings, we constructed two chimeric PSIs in sp. PCC 6803 demonstrating how unique structural features in photosynthetic complexes can change spectroscopic properties, allowing organisms to thrive under different environmental stresses. | |||||||||
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_21320.map.gz | 91.5 MB | EMDB map data format | |
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Header (meta data) | emd-21320-v30.xml emd-21320.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21320_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_21320.png | 97.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21320 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21320 | HTTPS FTP |
-Validation report
Summary document | emd_21320_validation.pdf.gz | 491 KB | Display | EMDB validaton report |
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Full document | emd_21320_full_validation.pdf.gz | 490.5 KB | Display | |
Data in XML | emd_21320_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_21320_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21320 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21320 | HTTPS FTP |
-Related structure data
Related structure data | 6vpvMC 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_21320.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: 1.05067 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 : Trimeric PSI from a High Light tolerant cyanobacteria, Cyanobacte...
+Supramolecule #1: Trimeric PSI from a High Light tolerant cyanobacteria, Cyanobacte...
+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: Photosystem I reaction center subunit II
+Macromolecule #5: Photosystem I reaction center subunit IV
+Macromolecule #6: PSI-F
+Macromolecule #7: Photosystem I reaction center subunit VIII
+Macromolecule #8: Photosystem I reaction center subunit IX
+Macromolecule #9: Photosystem I reaction center subunit PsaK
+Macromolecule #10: Photosystem I reaction center subunit XI
+Macromolecule #11: Photosystem I reaction center subunit XII
+Macromolecule #12: CHLOROPHYLL A ISOMER
+Macromolecule #13: CHLOROPHYLL A
+Macromolecule #14: PHYLLOQUINONE
+Macromolecule #15: IRON/SULFUR CLUSTER
+Macromolecule #16: BETA-CAROTENE
+Macromolecule #17: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #19: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.53 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 |