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Yorodumi- PDB-6kgx: Structure of the phycobilisome from the red alga Porphyridium pur... -
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Basic information
| Entry | Database: PDB / ID: 6kgx | ||||||
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| Title | Structure of the phycobilisome from the red alga Porphyridium purpureum | ||||||
 Components |
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 Keywords |  PHOTOSYNTHESIS / phycobilisome / Complex | ||||||
| Function / homology |  Function and homology informationphycobilisome / chloroplast thylakoid membrane / photosynthesis / lyase activitySimilarity search - Function | ||||||
| Biological species |  Porphyridium purpureum (eukaryote) | ||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
 Authors | Sui, S.F. / Ma, J.F. / 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. | ||||||
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Structure visualization
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| Structure viewer | Molecule: MolmilJmol/JSmol |
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Downloads & links
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| PDBx/mmCIF format | 6kgx.cif.gz | 21.1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb6kgx.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 6kgx.json.gz | Tree view | PDBx/mmJSON format | |
| Others |  Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/6kgxftp://data.pdbj.org/pub/pdb/validation_reports/kg/6kgx | HTTPS FTP |
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-Related structure data
| Related structure data |  9976MC  9977C  9978C  9979C  9980C  9981C  9982C  9983C  9984C  9985C  9986C  9987C  9988C M: map data used to model this data C: citing same article ( |
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| Similar structure data |
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PDBj-
Assembly
| Deposited unit | 
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-Components
-Protein , 17 types, 580 molecules A1C1E1G1I1K1N1P1R1T1V1X1c1e1g1i1k1m1p1r1t1v1x1z1O2Q2S2U2W2Z2...
| #1: Protein | Mass: 17824.029 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: E2IH77#2: Protein | Mass: 18584.182 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: P11393#3: Protein | Mass: 36924.992 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#4: Protein | Mass: 43968.605 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#5: Protein | Mass: 31332.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#6: Protein | Mass: 39727.625 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#7: Protein | Mass: 31792.982 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#11: Protein | Mass: 32886.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#12: Protein | Mass: 53601.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#13: Protein | Mass: 29453.639 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#14: Protein | Mass: 31358.787 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#15: Protein | Mass: 37175.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#16: Protein | Mass: 55146.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#21: Protein | Mass: 10428.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#23: Protein | Mass: 16915.260 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#24: Protein | Mass: 30272.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote)#25: Protein | Mass: 26620.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) |
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-Phycobilisome ... , 2 types, 8 molecules B2B6B7BBBFBIYH1H
| #8: Protein | Mass: 26996.689 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RZ90#22: Protein | Mass: 99468.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RZJ2 |
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-C-phycocyanin ... , 2 types, 72 molecules C2E2G2I2K2M2C6E6G6I6K6M6C7E7G7I7K7M7CBEBGBIBKBMBCFEFGFIFKFMF...
| #9: Protein | Mass: 17478.664 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RYI4#10: Protein | Mass: 18242.705 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RZB2 |
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-Allophycocyanin ... , 4 types, 46 molecules AHCHEHGHJHKHNHPHRHTHcHeHgHiHlHmHpHrHtHvHDHFHBHHHIHLHMHOHQHSH...
| #17: Protein | Mass: 17639.123 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RYM0#18: Protein | Mass: 17415.797 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0S279#19: Protein | Mass: 18126.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0S1U6#20: Protein | Mass: 19778.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RZE2 |
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-Non-polymers , 3 types, 1598 molecules 
| #26: Chemical | ChemComp-PEB / Phycoerythrobilin Mass: 588.694 Da / Num. of mol.: 1430 / Source method: obtained synthetically / Formula: C33H40N4O6#27: Chemical | ChemComp-PUB / Phycourobilin Mass: 590.710 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C33H42N4O6#28: Chemical | ChemComp-CYC / Phycocyanobilin Mass: 588.694 Da / Num. of mol.: 120 / Source method: obtained synthetically / Formula: C33H40N4O6 |
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-Details
| Has ligand of interest | N |
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-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: Complex of phycobilisome from red alga P.purpureum. / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL | ||||||||||||
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| Source (natural) | Organism: Porphyridium purpureum (eukaryote) | ||||||||||||
| Buffer solution | pH: 7 | ||||||||||||
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| Specimen | Conc.: 1.5 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
| EM embedding | Material: ice | ||||||||||||
| Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
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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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 0.001 mm / C2 aperture diameter: 70 µm |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Average exposure time: 5.6 sec. / Electron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 16218 |
| EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
| Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
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Processing
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| CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||
| Particle selection | Num. of particles selected: 686369 | ||||||||||||||||||
| Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||
| 3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191825 / Symmetry type: POINT |
