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Yorodumi- EMDB-9908: Structure of PSI-isiA supercomplex from Thermosynechococcus vulcanus -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9908 | |||||||||
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Title | Structure of PSI-isiA supercomplex from Thermosynechococcus vulcanus | |||||||||
Map data | ||||||||||
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 / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 ...: / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | |||||||||
Authors | Akita F / Nagao R / Kato K / Shen JR / Miyazaki N | |||||||||
Citation | Journal: Commun Biol / Year: 2020 Title: Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins. Authors: Fusamichi Akita / Ryo Nagao / Koji Kato / Yoshiki Nakajima / Makio Yokono / Yoshifumi Ueno / Takehiro Suzuki / Naoshi Dohmae / Jian-Ren Shen / Seiji Akimoto / Naoyuki Miyazaki / Abstract: Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its ...Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-Å resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI-IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI-IsiA supercomplex. | |||||||||
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_9908.map.gz | 36.8 MB | EMDB map data format | |
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Header (meta data) | emd-9908-v30.xml emd-9908.xml | 27 KB 27 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9908_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_9908.png | 102.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9908 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9908 | HTTPS FTP |
-Validation report
Summary document | emd_9908_validation.pdf.gz | 387.9 KB | Display | EMDB validaton report |
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Full document | emd_9908_full_validation.pdf.gz | 387.4 KB | Display | |
Data in XML | emd_9908_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_9908_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9908 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9908 | HTTPS FTP |
-Related structure data
Related structure data | 6k33MC 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_9908.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.113 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-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
+Macromolecule #10: Photosystem I reaction center subunit XI
+Macromolecule #11: Photosystem I reaction center subunit XII
+Macromolecule #12: Photosystem I reaction center subunit psaX
+Macromolecule #13: Iron stress in-duced protein A
+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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #21: CALCIUM ION
+Macromolecule #22: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 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 |