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Open data
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Basic information
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| Title | Local refinement of a PSI monomer of A. marina NIES-2412 | |||||||||||||||||||||
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Keywords | Photosystem I / Chlorophyll d / long wavelength / ELECTRON TRANSPORT | |||||||||||||||||||||
| Function / homology | Function and homology informationphotosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||||||||||||||
| Biological species | Acaryochloris marina (bacteria) / Acaryochloris marina NIES-2412 (bacteria) | |||||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.44 Å | |||||||||||||||||||||
Authors | Consoli G / Leong HF | |||||||||||||||||||||
| Funding support | Netherlands, European Union, United Kingdom, 6 items
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Citation | Journal: Sci Adv / Year: 2026Title: Far-red chlorophyll d clusters extend photosystem I absorption toward the red limit. Authors: Thomas J Oliver / Eduard Elias / Giovanni Consoli / Ho Fong Leong / Violeta Cordón-Preciado / Andrea Fantuzzi / Tanai Cardona / A William Rutherford / Roberta Croce / ![]() Abstract: Oxygenic photosynthesis is usually limited to visible light, but the marine cyanobacterium pushes this boundary by harvesting far-red photons with chlorophyll d. The best-studied strain, MBIC11017, ...Oxygenic photosynthesis is usually limited to visible light, but the marine cyanobacterium pushes this boundary by harvesting far-red photons with chlorophyll d. The best-studied strain, MBIC11017, unexpectedly lacks low-energy chlorophylls ("red forms") in photosystem I, limiting absorption beyond 740 nanometers. Here, we show that another strain, NIES-2412, has evolved a strategy to absorb far-red photons up to 760 nanometers. Combining time-resolved fluorescence spectroscopy with cryo-electron microscopy at 2.64-angstrom resolution, we identify two distinct classes of chlorophyll d red forms in its photosystem I. One class originates from classical charge-transfer-exciton mixing, while the other arises purely from excitonic interactions. Mapping all 96 chlorophylls d reveals the precise pigments responsible for these far-red states. We also uncover a previously unreported subunit, PsaX2, which stabilizes the photosystem I complex and shapes pigment geometry and energetics to enable the formation of red forms. Last, we show that the protein modifications responsible for binding and tuning these red forms are widespread across the genus but not within the model MBIC11017 strain. Far-red photons lie close to the energetic limit of oxygenic photosynthesis; their efficient use therefore requires fine-tuning of the photosynthetic machinery. To our knowledge, our findings provide the structural and mechanistic basis of one of the most red-shifted photosystem I complexes identified to date, highlighting a distinct adaptive strategy in far-red light environments and offering design principles for extending photosynthesis in crops into the infrared. | |||||||||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Header (meta data) | emd-54627-v30.xml emd-54627.xml | 32.5 KB 32.5 KB | Display Display | EMDB header |
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| FSC (resolution estimation) | emd_54627_fsc.xml | 19.6 KB | Display | FSC data file |
| Images | emd_54627.png | 73.6 KB | ||
| Map data | emd_54627.map.gz | 416.2 MB | EMDB map data format | |
| Filedesc metadata | emd-54627.cif.gz | 8.4 KB | ||
| Others | emd_54627_half_map_1.map.gz emd_54627_half_map_2.map.gz | 763.5 MB 763.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-54627 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-54627 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9s6pMC ![]() 54956 ![]() 9sk3C C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
-Supplemental data
-Half map: #2
| File | emd_54627_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_54627_half_map_2.map | ||||||||||||
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Sample components
+Entire : Photosystem I
+Supramolecule #1: Photosystem I
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #2: Photosystem I reaction center subunit II
+Macromolecule #3: Photosystem I reaction center subunit IV
+Macromolecule #4: Psa27 protein
+Macromolecule #5: Photosystem I reaction center subunit IX
+Macromolecule #6: Photosystem I reaction center subunit PsaK
+Macromolecule #7: PsaL
+Macromolecule #8: PsaM
+Macromolecule #9: PsaX2
+Macromolecule #10: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #11: Photosystem I iron-sulfur center
+Macromolecule #12: Photosystem I reaction center subunit III
+Macromolecule #13: CHLOROPHYLL D
+Macromolecule #14: PHEOPHYTIN A
+Macromolecule #15: PHYLLOQUINONE
+Macromolecule #16: (6'S)-beta,epsilon-carotene
+Macromolecule #17: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #18: IRON/SULFUR CLUSTER
+Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #20: CHLOROPHYLL D ISOMER
+Macromolecule #21: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 6.5 Details: 50 mM MES, 1 M betaine monohydrate, 20 mM CaCl2, 5 mM MgCl2 and 10% (v/v) glycerol, pH 6.5 adjusted with NaOH |
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| Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Acaryochloris marina (bacteria)
Authors
Netherlands, European Union,
United Kingdom, 6 items
Citation









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Processing
FIELD EMISSION GUN

