+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20963 | |||||||||
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Title | The structure of a red shifted photosystem I complex | |||||||||
Map data | Cryo EM map of a red shifted PSI from Synechocystis sp. PCC 6803 | |||||||||
Sample |
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Function / homology | Function and homology information plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) / Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) / Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Toporik H / Williams D / Chiu PL / Mazor Y | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: The structure of a red-shifted photosystem I reveals a red site in the core antenna. Authors: Hila Toporik / Anton Khmelnitskiy / Zachary Dobson / Reece Riddle / Dewight Williams / Su Lin / Ryszard Jankowiak / Yuval Mazor / Abstract: Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the ...Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I complex in Synechocystis PCC 6803 that shows enhanced absorption in the red spectral region. We combine Cryo-EM and spectroscopy to determine the structurefunction relationship in this red-shifted Photosystem I complex. Determining the structure of this complex reveals the precise architecture of the low energy site as well as large scale structural heterogeneity which is probably universal to all trimeric Photosystem I complexes. Identifying the structural elements that constitute red sites can expand the absorption spectrum of oxygenic photosynthetic and potentially modulate light harvesting efficiency. | |||||||||
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_20963.map.gz | 11.4 MB | EMDB map data format | |
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Header (meta data) | emd-20963-v30.xml emd-20963.xml | 24.5 KB 24.5 KB | Display Display | EMDB header |
Images | emd_20963.png | 255.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20963 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20963 | HTTPS FTP |
-Related structure data
Related structure data | 6uzvMC 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_20963.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo EM map of a red shifted PSI from Synechocystis sp. PCC 6803 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : PSI
+Supramolecule #1: PSI
+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: Photosystem I reaction center subunit III
+Macromolecule #7: Photosystem I reaction center subunit VIII
+Macromolecule #8: Photosystem I reaction center subunit IX
+Macromolecule #9: Photosystem I reaction center subunit XI
+Macromolecule #10: Photosystem I reaction center subunit XII
+Macromolecule #11: Photosystem I reaction center subunit PsaK 2
+Macromolecule #12: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #13: CHLOROPHYLL A ISOMER
+Macromolecule #14: CHLOROPHYLL A
+Macromolecule #15: PHYLLOQUINONE
+Macromolecule #16: IRON/SULFUR CLUSTER
+Macromolecule #17: BETA-CAROTENE
+Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #19: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #20: CALCIUM ION
-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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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 972010 |
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CTF correction | Software - Name: CTFFIND |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3) |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Software - details: 3 / Number images used: 196181 |