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Yorodumi- EMDB-24821: Structure of photosystem I with bound ferredoxin from Synechococc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24821 | |||||||||
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Title | Structure of photosystem I with bound ferredoxin from Synechococcus sp. PCC 7335 acclimated to far-red light | |||||||||
Map data | Sharpened map for Far-red light-acclimated PSI from Synechococcus sp. PCC 7335 | |||||||||
Sample |
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Keywords | Photosystem I / Far-red light photoacclimation / Chlorophyll f / Ferredoxin / PsaF / PsaJ / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechococcus sp. PCC 7335 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
Authors | Gisriel CJ / Flesher DA | |||||||||
Funding support | United States, 2 items
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Citation | Journal: J Biol Chem / Year: 2022 Title: Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation. Authors: Christopher J Gisriel / David A Flesher / Gaozhong Shen / Jimin Wang / Ming-Yang Ho / Gary W Brudvig / Donald A Bryant / Abstract: Far-red light photoacclimation exhibited by some cyanobacteria allows these organisms to use the far-red region of the solar spectrum (700-800 nm) for photosynthesis. Part of this process includes ...Far-red light photoacclimation exhibited by some cyanobacteria allows these organisms to use the far-red region of the solar spectrum (700-800 nm) for photosynthesis. Part of this process includes the replacement of six photosystem I (PSI) subunits with isoforms that confer the binding of chlorophyll (Chl) f molecules that absorb far-red light (FRL). However, the exact sites at which Chl f molecules are bound are still challenging to determine. To aid in the identification of Chl f-binding sites, we solved the cryo-EM structure of PSI from far-red light-acclimated cells of the cyanobacterium Synechococcus sp. PCC 7335. We identified six sites that bind Chl f with high specificity and three additional sites that are likely to bind Chl f at lower specificity. All of these binding sites are in the core-antenna regions of PSI, and Chl f was not observed among the electron transfer cofactors. This structural analysis also reveals both conserved and nonconserved Chl f-binding sites, the latter of which exemplify the diversity in FRL-PSI among species. We found that the FRL-PSI structure also contains a bound soluble ferredoxin, PetF1, at low occupancy, which suggests that ferredoxin binds less transiently than expected according to the canonical view of ferredoxin-binding to facilitate electron transfer. We suggest that this may result from structural changes in FRL-PSI that occur specifically during FRL photoacclimation. | |||||||||
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_24821.map.gz | 201.8 MB | EMDB map data format | |
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Header (meta data) | emd-24821-v30.xml emd-24821.xml | 28.1 KB 28.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24821_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_24821.png | 67.9 KB | ||
Filedesc metadata | emd-24821.cif.gz | 7.8 KB | ||
Others | emd_24821_additional_1.map.gz | 169.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24821 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24821 | HTTPS FTP |
-Validation report
Summary document | emd_24821_validation.pdf.gz | 596.3 KB | Display | EMDB validaton report |
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Full document | emd_24821_full_validation.pdf.gz | 595.9 KB | Display | |
Data in XML | emd_24821_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_24821_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24821 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24821 | HTTPS FTP |
-Related structure data
Related structure data | 7s3dMC 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_24821.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map for Far-red light-acclimated PSI from Synechococcus sp. PCC 7335 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map for Far-red light-acclimated PSI from Synechococcus...
File | emd_24821_additional_1.map | ||||||||||||
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Annotation | Unsharpened map for Far-red light-acclimated PSI from Synechococcus sp. PCC 7335 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
+Supramolecule #1: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #3: PsaC
+Macromolecule #4: Photosystem I 16 kDa polypeptide
+Macromolecule #5: Photosystem I reaction center subunit IV
+Macromolecule #6: PSI-F
+Macromolecule #7: PsaI2
+Macromolecule #8: Photosystem I reaction center subunit IX
+Macromolecule #9: Photosystem I reaction center subunit PsaK
+Macromolecule #10: PSI subunit V
+Macromolecule #11: PsaM
+Macromolecule #12: 2Fe-2S ferredoxin-type domain-containing protein
+Macromolecule #13: CHLOROPHYLL A ISOMER
+Macromolecule #14: CHLOROPHYLL A
+Macromolecule #15: Chlorophyll F
+Macromolecule #16: PHYLLOQUINONE
+Macromolecule #17: IRON/SULFUR CLUSTER
+Macromolecule #18: BETA-CAROTENE
+Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #20: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #21: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #22: CHLORIDE ION
+Macromolecule #23: CALCIUM ION
+Macromolecule #24: FE2/S2 (INORGANIC) CLUSTER
+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: 6.5 |
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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 K3 (6k x 4k) / Average electron dose: 40.8 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 |