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Yorodumi- EMDB-61519: Structural insights into the PSI-FCPI supercomplex from the cocco... -
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Open data
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Basic information
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| Title | Structural insights into the PSI-FCPI supercomplex from the coccolithophore Emiliania huxleyi | |||||||||
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Sample |
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Keywords | PSI-FCPI supercomplex / PHOTOSYNTHESIS | |||||||||
| Function / homology | Function and homology informationthylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding / membrane Similarity search - Function | |||||||||
| Biological species | Emiliania huxleyi CCMP1516 (eukaryote) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.79 Å | |||||||||
Authors | Shen LL / Li ZH / Wang WD | |||||||||
| Funding support | China, 1 items
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Citation | Journal: To Be PublishedTitle: Structural insights into the PSI-FCPI supercomplex from the coccolithophore Emiliania huxleyi Authors: Shen LL / Li ZH / Wang WD | |||||||||
| History |
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_61519.map.gz | 536.8 MB | EMDB map data format | |
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| Header (meta data) | emd-61519-v30.xml emd-61519.xml | 60.8 KB 60.8 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_61519_fsc.xml | 21.8 KB | Display | FSC data file |
| Images | emd_61519.png | 126.8 KB | ||
| Filedesc metadata | emd-61519.cif.gz | 12.9 KB | ||
| Others | emd_61519_half_map_1.map.gz emd_61519_half_map_2.map.gz | 1016.4 MB 1016.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-61519 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-61519 | HTTPS FTP |
-Validation report
| Summary document | emd_61519_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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| Full document | emd_61519_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | emd_61519_validation.xml.gz | 31.2 KB | Display | |
| Data in CIF | emd_61519_validation.cif.gz | 41.5 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-61519 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-61519 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9jj8MC M: atomic model generated by this map C: citing same article ( |
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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
| File | Download / File: emd_61519.map.gz / Format: CCP4 / Size: 1.1 GB / 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: 0.808 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_61519_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_61519_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Eh-PSI-FCPI
+Supramolecule #1: Eh-PSI-FCPI
+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 III
+Macromolecule #7: Photosystem I reaction center subunit VIII
+Macromolecule #8: Photosystem I reaction center subunit IX
+Macromolecule #9: Photosystem I reaction center subunit XI
+Macromolecule #10: Photosystem I reaction center subunit XII
+Macromolecule #11: PSI-K
+Macromolecule #12: Linker-protein
+Macromolecule #13: Light harvesting protein
+Macromolecule #14: Light harvesting protein
+Macromolecule #15: Light harvesting protein
+Macromolecule #16: Light harvesting protein
+Macromolecule #17: Light harvesting protein
+Macromolecule #18: Light harvesting protein
+Macromolecule #19: Light harvesting protein
+Macromolecule #20: Light harvesting protein
+Macromolecule #21: Light harvesting protein
+Macromolecule #22: Light harvesting protein
+Macromolecule #23: Light harvesting protein
+Macromolecule #24: Light harvesting protein
+Macromolecule #25: Light harvesting protein
+Macromolecule #26: Light harvesting protein
+Macromolecule #27: Light harvesting protein
+Macromolecule #28: Light harvesting protein
+Macromolecule #29: Light harvesting protein
+Macromolecule #30: Light harvesting protein
+Macromolecule #31: Light harvesting protein
+Macromolecule #32: Light harvesting protein
+Macromolecule #33: Light harvesting protein
+Macromolecule #34: Light harvesting protein
+Macromolecule #35: Light harvesting protein
+Macromolecule #36: Light harvesting protein
+Macromolecule #37: PsaR
+Macromolecule #38: Light harvesting protein
+Macromolecule #39: CHLOROPHYLL A
+Macromolecule #40: PHYLLOQUINONE
+Macromolecule #41: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #42: BETA-CAROTENE
+Macromolecule #43: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...
+Macromolecule #44: IRON/SULFUR CLUSTER
+Macromolecule #45: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #46: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #47: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #48: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
+Macromolecule #49: Chlorophyll c2
+Macromolecule #50: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-2-[2-[(4~{S},6~{R...
+Macromolecule #51: Chlorophyll C3
+Macromolecule #52: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})...
-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 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TALOS ARCTICA |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Emiliania huxleyi CCMP1516 (eukaryote)
Authors
China, 1 items
Citation









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Processing
FIELD EMISSION GUN

