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Yorodumi- EMDB-34529: Un-sharpened map of phycobilisome from Porphyridium purpureum und... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34529 | |||||||||
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Title | Un-sharpened map of phycobilisome from Porphyridium purpureum under low light | |||||||||
Map data | Low Light unsharpen map | |||||||||
Sample |
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Keywords | phycobilisome / Complex / PHOTOSYNTHESIS | |||||||||
Biological species | Porphyridium purpureum (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.74 Å | |||||||||
Authors | Sui SF / Ma JF | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34529.map.gz | 606.8 MB | EMDB map data format | |
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Header (meta data) | emd-34529-v30.xml emd-34529.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
Images | emd_34529.png | 116.4 KB | ||
Filedesc metadata | emd-34529.cif.gz | 4.2 KB | ||
Others | emd_34529_half_map_1.map.gz emd_34529_half_map_2.map.gz | 614.2 MB 614.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34529 | HTTPS FTP |
-Related structure data
Related structure data | 9976C 9977C 9978C 9979C 9980C 9981C 9982C 9983C 9984C 9985C 9986C 9987C 9988C 6kgxC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34529.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Low Light unsharpen map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Low Light unsharpen map half2
File | emd_34529_half_map_1.map | ||||||||||||
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Annotation | Low Light unsharpen map_half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Low Light unsharpen map half1
File | emd_34529_half_map_2.map | ||||||||||||
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Annotation | Low Light unsharpen map_half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of phycobilisome from red alga P.purpureum.
Entire | Name: Complex of phycobilisome from red alga P.purpureum. |
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Components |
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-Supramolecule #1: Complex of phycobilisome from red alga P.purpureum.
Supramolecule | Name: Complex of phycobilisome from red alga P.purpureum. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25 |
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Source (natural) | Organism: Porphyridium purpureum (eukaryote) |
-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 | |||||||||
Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5 | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy / Cs: 0.001 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 686369 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 157785 |