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Yorodumi- EMDB-9976: Structure of the phycobilisome from the red alga Porphyridium pur... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9976 | |||||||||
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Title | Structure of the phycobilisome from the red alga Porphyridium purpureum | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information phycobilisome / chloroplast thylakoid membrane / photosynthesis / lyase activity Similarity search - Function | |||||||||
Biological species | Porphyridium purpureum (eukaryote) / Red alga (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Sui SF / Ma JF / You X / Sun S | |||||||||
Citation | Journal: Nature / Year: 2020 Title: Structural basis of energy transfer in Porphyridium purpureum phycobilisome. Authors: Jianfei Ma / Xin You / Shan Sun / Xiaoxiao Wang / Song Qin / Sen-Fang Sui / Abstract: Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments. Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red ...Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments. Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae, although how the energies of the chromophores within these complexes are modulated by their environment is unclear. Here we report the cryo-electron microscopy structure of a 14.7-megadalton phycobilisome with a hemiellipsoidal shape from the red alga Porphyridium purpureum. Within this complex we determine the structures of 706 protein subunits, including 528 phycoerythrin, 72 phycocyanin, 46 allophycocyanin and 60 linker proteins. In addition, 1,598 chromophores are resolved comprising 1,430 phycoerythrobilin, 48 phycourobilin and 120 phycocyanobilin molecules. The markedly improved resolution of our structure compared with that of the phycobilisome of Griffithsia pacifica enabled us to build an accurate atomic model of the P. purpureum phycobilisome system. The model reveals how the linker proteins affect the microenvironment of the chromophores, and suggests that interactions of the aromatic amino acids of the linker proteins with the chromophores may be a key factor in fine-tuning the energy states of the chromophores to ensure the efficient unidirectional transfer of energy. | |||||||||
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_9976.map.gz | 118.3 MB | EMDB map data format | |
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Header (meta data) | emd-9976-v30.xml emd-9976.xml | 37.5 KB 37.5 KB | Display Display | EMDB header |
Images | emd_9976.png | 113 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9976 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9976 | HTTPS FTP |
-Validation report
Summary document | emd_9976_validation.pdf.gz | 437.3 KB | Display | EMDB validaton report |
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Full document | emd_9976_full_validation.pdf.gz | 436.9 KB | Display | |
Data in XML | emd_9976_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | emd_9976_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9976 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9976 | HTTPS FTP |
-Related structure data
Related structure data | 6kgxMC 7lixM 7liyM 7lizM 7lj0M 9977C 9978C 9979C 9980C 9981C 9982C 9983C 9984C 9985C 9986C 9987C 9988C 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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-Map
File | Download / File: emd_9976.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Complex of phycobilisome from red alga P.purpureum.
+Supramolecule #1: Complex of phycobilisome from red alga P.purpureum.
+Macromolecule #1: Phycoerythrin alpha subunit
+Macromolecule #2: B-phycoerythrin beta chain
+Macromolecule #3: LR7
+Macromolecule #4: LR2_Hb
+Macromolecule #5: LR9
+Macromolecule #6: LR1
+Macromolecule #7: LR4
+Macromolecule #8: Phycobilisome rod-core linker polypeptide
+Macromolecule #9: C-phycocyanin alpha subunit
+Macromolecule #10: C-phycocyanin beta subunit
+Macromolecule #11: LR2
+Macromolecule #12: LRC2
+Macromolecule #13: LR5
+Macromolecule #14: LR8
+Macromolecule #15: LR3
+Macromolecule #16: LRC3
+Macromolecule #17: Allophycocyanin alpha subunit
+Macromolecule #18: Allophycocyanin beta subunit
+Macromolecule #19: Allophycocyanin gamma subunit
+Macromolecule #20: Allophycocyanin beta 18 subunit
+Macromolecule #21: LC
+Macromolecule #22: Phycobilisome linker polypeptide
+Macromolecule #23: LRC4
+Macromolecule #24: LRC5
+Macromolecule #25: LRC6
+Macromolecule #26: PHYCOERYTHROBILIN
+Macromolecule #27: PHYCOUROBILIN
+Macromolecule #28: PHYCOCYANOBILIN
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | ||||||
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Buffer | pH: 7 Component:
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Sugar embedding | Material: ice | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number real images: 16218 / Average exposure time: 5.6 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |