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Yorodumi- EMDB-31605: Cryo-EM structure of cyanobacterial photosystem I in the presence... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31605 | |||||||||
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Title | Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6 | |||||||||
Map data | 3D refined map in C3 symmetry, which was used for model building and refinement. | |||||||||
Sample |
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Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding ...photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) / Thermosynechococcus vestitus BP-1 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.97 Å | |||||||||
Authors | Li J / Kurisu G | |||||||||
Funding support | 1 items
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Citation | Journal: Commun Biol / Year: 2022 Title: Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 Å resolution. Authors: Jiannan Li / Noriyuki Hamaoka / Fumiaki Makino / Akihiro Kawamoto / Yuxi Lin / Matthias Rögner / Marc M Nowaczyk / Young-Ho Lee / Keiichi Namba / Christoph Gerle / Genji Kurisu / Abstract: Photosystem I (PSI) is a light driven electron pump transferring electrons from Cytochrome c (Cyt c) to Ferredoxin (Fd). An understanding of this electron transfer process is hampered by a paucity of ...Photosystem I (PSI) is a light driven electron pump transferring electrons from Cytochrome c (Cyt c) to Ferredoxin (Fd). An understanding of this electron transfer process is hampered by a paucity of structural detail concerning PSI:Fd interface and the possible binding sites of Cyt c. Here we describe the high resolution cryo-EM structure of Thermosynechococcus elongatus BP-1 PSI in complex with Fd and a loosely bound Cyt c. Side chain interactions at the PSI:Fd interface including bridging water molecules are visualized in detail. The structure explains the properties of mutants of PsaE and PsaC that affect kinetics of Fd binding and suggests a molecular switch for the dissociation of Fd upon reduction. Calorimetry-based thermodynamic analyses confirms a single binding site for Fd and demonstrates that PSI:Fd complexation is purely driven by entropy. A possible reaction cycle for the efficient transfer of electrons from Cyt c to Fd via PSI is proposed. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31605.map.gz | 193.3 MB | EMDB map data format | |
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Header (meta data) | emd-31605-v30.xml emd-31605.xml | 38.1 KB 38.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31605_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_31605.png | 57 KB | ||
Masks | emd_31605_msk_1.map | 244.1 MB | Mask map | |
Others | emd_31605_additional_1.map.gz emd_31605_additional_2.map.gz emd_31605_half_map_1.map.gz emd_31605_half_map_2.map.gz | 227.8 MB 172.9 MB 194.8 MB 194.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31605 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31605 | HTTPS FTP |
-Validation report
Summary document | emd_31605_validation.pdf.gz | 799.8 KB | Display | EMDB validaton report |
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Full document | emd_31605_full_validation.pdf.gz | 799.3 KB | Display | |
Data in XML | emd_31605_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_31605_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31605 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31605 | HTTPS FTP |
-Related structure data
Related structure data | 7fixMC 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_31605.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 3D refined map in C3 symmetry, which was used for model building and refinement. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.806 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_31605_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Post-process map in C3 symmetry. (Resolution: 1.97 A)
File | emd_31605_additional_1.map | ||||||||||||
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Annotation | Post-process map in C3 symmetry. (Resolution: 1.97 A) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Post-process map in C1 symmetry. (Resolution: 2.08 A)
File | emd_31605_additional_2.map | ||||||||||||
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Annotation | Post-process map in C1 symmetry. (Resolution: 2.08 A) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of 3D refine.
File | emd_31605_half_map_1.map | ||||||||||||
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Annotation | Half map of 3D refine. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of 3D refine.
File | emd_31605_half_map_2.map | ||||||||||||
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Annotation | Half map of 3D refine. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM map of cyanobacterial photosystem I in the presence of fe...
+Supramolecule #1: Cryo-EM map of cyanobacterial photosystem I in the presence of fe...
+Supramolecule #2: Photosystem I trimer
+Supramolecule #3: Ga-Substituted Ferredoxin
+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
+Macromolecule #10: Photosystem I reaction center subunit XI
+Macromolecule #11: Photosystem I reaction center subunit XII
+Macromolecule #12: Ferredoxin-1
+Macromolecule #13: Photosystem I 4.8K protein
+Macromolecule #14: CHLOROPHYLL A ISOMER
+Macromolecule #15: CHLOROPHYLL A
+Macromolecule #16: PHYLLOQUINONE
+Macromolecule #17: IRON/SULFUR CLUSTER
+Macromolecule #18: BETA-CAROTENE
+Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #20: UNKNOWN LIGAND
+Macromolecule #21: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #22: CALCIUM ION
+Macromolecule #23: [2Ga-2S] cluster
+Macromolecule #24: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 30 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 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: 1.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |