|Entry||Database: EMDB / ID: EMD-9982|
|Title||Local map of the Re region of the phycobilisome from the red alga P. purpureum|
|Sample||Local map of the Re region of the phycobilisome from the red alga P. purpureum|
|Biological species||Porphyridium purpureum (eukaryote)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.04 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.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_9982.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.091 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Local map of the Re region of the phycobilisome from the red alga...
|Entire||Name: Local map of the Re region of the phycobilisome from the red alga P. purpureum|
Number of components: 1
-Component #1: protein, Local map of the Re region of the phycobilisome from the...
|Protein||Name: Local map of the Re region of the phycobilisome from the red alga P. purpureum|
Recombinant expression: No
|Source||Species: Porphyridium purpureum (eukaryote)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1.5 mg/mL / pH: 7|
|Vitrification||Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 105000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 2200.0 nm / Energy filter: GIF Quantum LS|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 16218|
|Processing||Method: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 191825|
|3D reconstruction||Software: RELION / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF|
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