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Yorodumi- EMDB-0727: Structure of PSI from H. hongdechloris grown under far-red light ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0727 | |||||||||
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Title | Structure of PSI from H. hongdechloris grown under far-red light condition | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Photosystem I / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information thylakoid membrane / : / 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 ...thylakoid membrane / : / 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 / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Halomicronema hongdechloris (bacteria) / Halomicronema hongdechloris C2206 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.41 Å | |||||||||
Authors | Kato K / Nagao R | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for the adaptation and function of chlorophyll f in photosystem I. Authors: Koji Kato / Toshiyuki Shinoda / Ryo Nagao / Seiji Akimoto / Takehiro Suzuki / Naoshi Dohmae / Min Chen / Suleyman I Allakhverdiev / Jian-Ren Shen / Fusamichi Akita / Naoyuki Miyazaki / Tatsuya Tomo / Abstract: Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first ...Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f. | |||||||||
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_0727.map.gz | 23.7 MB | EMDB map data format | |
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Header (meta data) | emd-0727-v30.xml emd-0727.xml | 23.9 KB 23.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0727_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_0727.png | 98.7 KB | ||
Filedesc metadata | emd-0727.cif.gz | 7.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0727 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0727 | HTTPS FTP |
-Validation report
Summary document | emd_0727_validation.pdf.gz | 470 KB | Display | EMDB validaton report |
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Full document | emd_0727_full_validation.pdf.gz | 469.6 KB | Display | |
Data in XML | emd_0727_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | emd_0727_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0727 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0727 | HTTPS FTP |
-Related structure data
Related structure data | 6kmxMC 0726C 6kmwC 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_0727.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.87 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 : far-red PSI
+Supramolecule #1: far-red 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 VIII
+Macromolecule #7: Photosystem I reaction center subunit PsaK
+Macromolecule #8: Photosystem I reaction center subunit XI
+Macromolecule #9: Photosystem I reaction center subunit XII
+Macromolecule #10: CHLOROPHYLL A ISOMER
+Macromolecule #11: CHLOROPHYLL A
+Macromolecule #12: Chlorophyll F
+Macromolecule #13: PHYLLOQUINONE
+Macromolecule #14: IRON/SULFUR CLUSTER
+Macromolecule #15: BETA-CAROTENE
+Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #17: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #19: UNKNOWN LIGAND
+Macromolecule #20: CALCIUM ION
+Macromolecule #21: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.071 mg/mL | ||||||
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Buffer | pH: 6.5 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. | ||||||
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) / Detector mode: COUNTING / Average electron dose: 47.0 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 |