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Yorodumi- EMDB-26601: Energetic robustness to large scale structural dynamics in a phot... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26601 | |||||||||
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Title | Energetic robustness to large scale structural dynamics in a photosynthetic supercomplex | |||||||||
Map data | PSI-IsiA complex | |||||||||
Sample |
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Keywords | photosystem I / antenna / cyanobacteria / photosynthesis / membrane complex | |||||||||
Function / homology | Function and homology information plasma membrane-derived photosystem I / cellular response to iron ion starvation / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport chain / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis ...plasma membrane-derived photosystem I / cellular response to iron ion starvation / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport chain / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Harris D / Toporik H / Schlau-Cohen GS / Mazor Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Energetic robustness to large scale structural fluctuations in a photosynthetic supercomplex. Authors: Dvir Harris / Hila Toporik / Gabriela S Schlau-Cohen / Yuval Mazor / Abstract: Photosynthetic organisms transport and convert solar energy with near-unity quantum efficiency using large protein supercomplexes held in flexible membranes. The individual proteins position ...Photosynthetic organisms transport and convert solar energy with near-unity quantum efficiency using large protein supercomplexes held in flexible membranes. The individual proteins position chlorophylls to tight tolerances considered critical for fast and efficient energy transfer. The variability in protein organization within the supercomplexes, and how efficiency is maintained despite variability, had been unresolved. Here, we report on structural heterogeneity in the 2-MDa cyanobacterial PSI-IsiA photosynthetic supercomplex observed using Cryo-EM, revealing large-scale variances in the positions of IsiA relative to PSI. Single-molecule measurements found efficient IsiA-to-PSI energy transfer across all conformations, along with signatures of transiently decoupled IsiA. Structure based calculations showed that rapid IsiA-to-PSI energy transfer is always maintained, and even increases by three-fold in rare conformations via IsiA-specific chls. We postulate that antennae design mitigates structural fluctuations, providing a mechanism for robust energy transfer in the flexible membrane. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26601.map.gz | 224 MB | EMDB map data format | |
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Header (meta data) | emd-26601-v30.xml emd-26601.xml | 27.4 KB 27.4 KB | Display Display | EMDB header |
Images | emd_26601.png | 94.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26601 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26601 | HTTPS FTP |
-Validation report
Summary document | emd_26601_validation.pdf.gz | 541.7 KB | Display | EMDB validaton report |
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Full document | emd_26601_full_validation.pdf.gz | 541.3 KB | Display | |
Data in XML | emd_26601_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | emd_26601_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26601 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26601 | HTTPS FTP |
-Related structure data
Related structure data | 7umhMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26601.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | PSI-IsiA complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : PSI-IsiA
+Supramolecule #1: PSI-IsiA
+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 PsaK 1
+Macromolecule #10: Photosystem I reaction center subunit XI
+Macromolecule #11: Photosystem I reaction center subunit XII
+Macromolecule #12: Iron stress-induced chlorophyll-binding protein
+Macromolecule #13: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #14: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #15: CHLOROPHYLL A ISOMER
+Macromolecule #16: CHLOROPHYLL A
+Macromolecule #17: PHYLLOQUINONE
+Macromolecule #18: IRON/SULFUR CLUSTER
+Macromolecule #19: BETA-CAROTENE
+Macromolecule #20: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #21: beta,beta-caroten-4-one
+Macromolecule #22: CALCIUM ION
+Macromolecule #23: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #24: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #25: water
-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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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |