+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10995 | |||||||||
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Title | Dunaliella Minimal Photosystem I | |||||||||
Map data | ||||||||||
Sample |
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Keywords | membrane complex / photosystem I / dunaliella / light harvesting / excitation transfer / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information photosynthesis, light harvesting / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / photosystem II / chloroplast thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosynthesis, light harvesting / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / photosystem II / chloroplast thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Dunaliella salina (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Nelson N / Caspy I | |||||||||
Funding support | Israel, Belgium, 2 items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2020 Title: Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex. Authors: Ido Caspy / Tirupathi Malavath / Daniel Klaiman / Maria Fadeeva / Yoel Shkolnisky / Nathan Nelson / Abstract: Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained ...Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained for the complexes that were isolated from various organisms, ranging from cyanobacteria to plants. These complexes are all evolutionarily linked. In this paper, the researchers have uncovered the increased complexity of PSI in a single organism demonstrated by the coexistance of two distinct PSI compositions. The Large Dunaliella PSI contains eight additional subunits, six in PSI core and two light harvesting complexes. Two additional chlorophyll a molecules pertinent for efficient excitation energy transfer in state II transition were identified in PsaL and PsaO. Short distances between these newly identified chlorophylls correspond with fast excitation transfer rates previously reported during state II transition. The apparent PSI conformations could be a coping mechanism for the high salinity. | |||||||||
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_10995.map.gz | 166.8 MB | EMDB map data format | |
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Header (meta data) | emd-10995-v30.xml emd-10995.xml | 30.2 KB 30.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10995_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_10995.png | 147.7 KB | ||
Filedesc metadata | emd-10995.cif.gz | 8.1 KB | ||
Others | emd_10995_half_map_1.map.gz emd_10995_half_map_2.map.gz | 140.8 MB 140.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10995 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10995 | HTTPS FTP |
-Validation report
Summary document | emd_10995_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_10995_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_10995_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | emd_10995_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10995 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10995 | HTTPS FTP |
-Related structure data
Related structure data | 6yxrMC 6sl5C 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_10995.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_10995_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10995_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Large dunaliella salina photosystem I-LHC supercomplex
+Supramolecule #1: Large dunaliella salina photosystem I-LHC supercomplex
+Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #2: Lhca2
+Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #4: Lhca4
+Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #7: Photosystem I iron-sulfur center
+Macromolecule #8: PsaD
+Macromolecule #9: PsaE
+Macromolecule #10: PsaF
+Macromolecule #11: Photosystem I reaction center subunit IX
+Macromolecule #12: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #13: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #14: BETA-CAROTENE
+Macromolecule #15: CHLOROPHYLL A
+Macromolecule #16: CHLOROPHYLL B
+Macromolecule #17: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #19: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
+Macromolecule #20: CHLOROPHYLL A ISOMER
+Macromolecule #21: PHYLLOQUINONE
+Macromolecule #22: IRON/SULFUR CLUSTER
+Macromolecule #23: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
-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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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: 2.5 sec blotting before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4306 / Average electron dose: 42.68 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6yxr: |