+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11588 | |||||||||
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Title | Structure of low-light grown Chlorella ohadii Photosystem I | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information malate transport / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / acyltransferase activity, transferring groups other than amino-acyl groups ...malate transport / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / acyltransferase activity, transferring groups other than amino-acyl groups / chlorophyll binding / chloroplast thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosynthesis / cell redox homeostasis / monooxygenase activity / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / protein kinase activity / iron ion binding / protein phosphorylation / heme binding / magnesium ion binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Chlorella ohadii (plant) / Freshwater green alga (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Caspy I / Nelson N / Nechushtai R / Neumann E / Shkolnisky Y | |||||||||
Funding support | Israel, 2 items
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Citation | Journal: Nat Plants / Year: 2021 Title: Cryo-EM photosystem I structure reveals adaptation mechanisms to extreme high light in Chlorella ohadii. Authors: Ido Caspy / Ehud Neumann / Maria Fadeeva / Varda Liveanu / Anton Savitsky / Anna Frank / Yael Levi Kalisman / Yoel Shkolnisky / Omer Murik / Haim Treves / Volker Hartmann / Marc M Nowaczyk / ...Authors: Ido Caspy / Ehud Neumann / Maria Fadeeva / Varda Liveanu / Anton Savitsky / Anna Frank / Yael Levi Kalisman / Yoel Shkolnisky / Omer Murik / Haim Treves / Volker Hartmann / Marc M Nowaczyk / Wolfgang Schuhmann / Matthias Rögner / Itamar Willner / Aaron Kaplan / Gadi Schuster / Nathan Nelson / Wolfgang Lubitz / Rachel Nechushtai / Abstract: Photosynthesis in deserts is challenging since it requires fast adaptation to rapid night-to-day changes, that is, from dawn's low light (LL) to extreme high light (HL) intensities during the daytime. ...Photosynthesis in deserts is challenging since it requires fast adaptation to rapid night-to-day changes, that is, from dawn's low light (LL) to extreme high light (HL) intensities during the daytime. To understand these adaptation mechanisms, we purified photosystem I (PSI) from Chlorella ohadii, a green alga that was isolated from a desert soil crust, and identified the essential functional and structural changes that enable the photosystem to perform photosynthesis under extreme high light conditions. The cryo-electron microscopy structures of PSI from cells grown under low light (PSI) and high light (PSI), obtained at 2.70 and 2.71 Å, respectively, show that part of light-harvesting antenna complex I (LHCI) and the core complex subunit (PsaO) are eliminated from PSI to minimize the photodamage. An additional change is in the pigment composition and their number in LHCI; about 50% of chlorophyll b is replaced by chlorophyll a. This leads to higher electron transfer rates in PSI and might enable C. ohadii PSI to act as a natural photosynthesiser in photobiocatalytic systems. PSI or PSI were attached to an electrode and their induced photocurrent was determined. To obtain photocurrents comparable with PSI, 25 times the amount of PSI was required, demonstrating the high efficiency of PSI. Hence, we suggest that C. ohadii PSI is an ideal candidate for the design of desert artificial photobiocatalytic systems. | |||||||||
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_11588.map.gz | 395.2 MB | EMDB map data format | |
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Header (meta data) | emd-11588-v30.xml emd-11588.xml | 49.8 KB 49.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11588_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_11588.png | 180.4 KB | ||
Others | emd_11588_half_map_1.map.gz emd_11588_half_map_2.map.gz | 338.2 MB 338.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11588 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11588 | HTTPS FTP |
-Related structure data
Related structure data | 6zzxMC 6zzyC 7a4pC 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_11588.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: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_11588_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11588_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosystem I
+Supramolecule #1: Photosystem I
+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 chloroplastic
+Macromolecule #5: Photosystem I reaction center subunit IV
+Macromolecule #6: PSI-F
+Macromolecule #7: Photosystem I reaction center subunit chloroplastic
+Macromolecule #8: Photosystem I reaction center subunit VI-chloroplastic-like
+Macromolecule #9: Photosystem I reaction center subunit IX
+Macromolecule #10: Photosystem I reaction center subunit chloroplastic
+Macromolecule #11: Photosystem I reaction center subunit XI
+Macromolecule #12: Photosystem I reaction center subunit XII
+Macromolecule #13: Photosystem I reaction center subunit VIII
+Macromolecule #14: Photosystem I subunit O
+Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #16: Glutathione reductase
+Macromolecule #17: Lhca4
+Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #19: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #20: Lhca7
+Macromolecule #21: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #22: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #23: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #24: CHLOROPHYLL A ISOMER
+Macromolecule #25: CHLOROPHYLL A
+Macromolecule #26: CHLOROPHYLL B
+Macromolecule #27: PHYLLOQUINONE
+Macromolecule #28: IRON/SULFUR CLUSTER
+Macromolecule #29: BETA-CAROTENE
+Macromolecule #30: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #31: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #32: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #33: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #34: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
+Macromolecule #35: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #36: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #37: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #38: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypro...
+Macromolecule #39: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+Macromolecule #40: (3R)-beta,beta-caroten-3-ol
+Macromolecule #41: SPHINGOSINE
+Macromolecule #42: beta,beta-caroten-4-one
+Macromolecule #43: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #44: ASTAXANTHIN
+Macromolecule #45: OLEIC ACID
+Macromolecule #46: (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl...
+Macromolecule #47: PALMITIC ACID
+Macromolecule #48: DIACYL GLYCEROL
+Macromolecule #49: benzene-1,3,5-triol
+Macromolecule #50: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #51: Tripalmitoylglycerol
+Macromolecule #52: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...
+Macromolecule #53: [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETH...
+Macromolecule #54: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 4 / Number real images: 4926 / Average exposure time: 1.4 sec. / Average electron dose: 49.05 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |