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- EMDB-9976: Structure of the phycobilisome from the red alga Porphyridium pur... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9976 | |||||||||
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Title | Structure of the phycobilisome from the red alga Porphyridium purpureum | |||||||||
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Function / homology | ![]() phycobilisome / chloroplast thylakoid membrane / photosynthesis / lyase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Sui SF / Ma JF / You X / Sun S | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 118.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 37.5 KB 37.5 KB | Display Display | ![]() |
Images | ![]() | 113 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 437.3 KB | Display | ![]() |
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Full document | ![]() | 436.9 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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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
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |