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- EMDB-11640: Structure of small high-light grown Chlorella ohadii photosystem I -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11640 | |||||||||
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Title | Structure of small high-light grown Chlorella ohadii photosystem I | |||||||||
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![]() | photosystem I / light stress / PHOTOSYNTHESIS | |||||||||
Function / homology | ![]() malate transport / glutathione-disulfide reductase (NADPH) activity / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosystem II / acyltransferase activity, transferring groups other than amino-acyl groups ...malate transport / glutathione-disulfide reductase (NADPH) activity / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosystem II / acyltransferase activity, transferring groups other than amino-acyl groups / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / monooxygenase activity / glutathione metabolic process / chloroplast / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / iron ion binding / heme binding / magnesium ion binding / mitochondrion / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Caspy I / Nelson N | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 479.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 46.4 KB 46.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.2 KB | Display | ![]() |
Images | ![]() | 114.8 KB | ||
Filedesc metadata | ![]() | 10.6 KB | ||
Others | ![]() ![]() | 410.5 MB 411 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a4pMC ![]() 6zzxC ![]() 6zzyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.81 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_11640_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11640_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Small high light grown Chlorella ohadii photosystem I
+Supramolecule #1: Small high light grown Chlorella ohadii 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 IX
+Macromolecule #9: PSI-K
+Macromolecule #10: Photosystem I reaction center subunit XII
+Macromolecule #11: Photosystem I reaction center subunit VIII
+Macromolecule #12: PSI subunit V
+Macromolecule #13: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #14: Glutathione reductase
+Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #19: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #20: Photosystem I reaction center subunit VI-chloroplastic-like
+Macromolecule #21: CHLOROPHYLL A ISOMER
+Macromolecule #22: CHLOROPHYLL A
+Macromolecule #23: PHYLLOQUINONE
+Macromolecule #24: BETA-CAROTENE
+Macromolecule #25: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #26: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #27: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
+Macromolecule #28: IRON/SULFUR CLUSTER
+Macromolecule #29: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #30: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #31: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #32: [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETH...
+Macromolecule #33: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #34: ERGOSTEROL
+Macromolecule #35: (3R)-beta,beta-caroten-3-ol
+Macromolecule #36: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypro...
+Macromolecule #37: beta,beta-caroten-4-one
+Macromolecule #38: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #39: CHLOROPHYLL B
+Macromolecule #40: OLEIC ACID
+Macromolecule #41: (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl...
+Macromolecule #42: 2-(2-azanylethanoylamino)ethanoic acid
+Macromolecule #43: PALMITIC ACID
+Macromolecule #44: DIACYL GLYCEROL
+Macromolecule #45: SPHINGOSINE
+Macromolecule #46: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #47: Tripalmitoylglycerol
+Macromolecule #48: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...
+Macromolecule #49: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 10280 / Average electron dose: 46.04 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 165000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |