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Yorodumi- PDB-7lj0: Linker 3 and scaffolded phycoerythrin beta subunit from the phyco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lj0 | ||||||||||||
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Title | Linker 3 and scaffolded phycoerythrin beta subunit from the phycobilisome of Porphyridium purpureum | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / linker / phycobilisome / PBS / light harvesting / red algae / scaffolding | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Porphyridium purpureum (eukaryote) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
Authors | Rathbone, H.W. / Landsberg, M.J. / Michie, K.A. / Green, B.R. / Curmi, P.M.G. | ||||||||||||
Funding support | Australia, United States, 3items
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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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Remark 0 | THIS DEPOSITION 7LJ0 PROVIDES A STRUCTURAL MODEL FOR PREVIOUSLY UNMODELED EM MAP DENSITY IN EMD- ...THIS DEPOSITION 7LJ0 PROVIDES A STRUCTURAL MODEL FOR PREVIOUSLY UNMODELED EM MAP DENSITY IN EMD-9976. THIS IS NOT A REPLACEMENT, ONLY AN ADDITION. ORIGINAL AUTHORS OF EMD-9976 ARE SUI, S.F., MA, J.F., YOU, X., SUN, S. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lj0.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lj0.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 7lj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/7lj0 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/7lj0 | HTTPS FTP |
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-Related structure data
Related structure data | 9976M 7lixC 7liyC 7lizC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 34958.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z323 | ||
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#2: Protein | Mass: 18584.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: P11393 | ||
#3: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Phycobilisome / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Porphyridium purpureum (eukaryote) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: ice |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191825 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.75 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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