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Yorodumi- PDB-7efv: Crystal structure of octameric state of C-phycocyanin from Thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7efv | ||||||||||||
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Title | Crystal structure of octameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77 | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / light-harvesting complex | ||||||||||||
Function / homology | Function and homology information : / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||||||||
Biological species | Leptolyngbya sp. O-77 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||||||||
Authors | Minato, T. / Teramoto, T. / Hung, N.K. / Yamada, K. / Ogo, S. / Kakuta, Y. / Yoon, K.S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Commun Biol / Year: 2021 Title: Non-conventional octameric structure of C-phycocyanin. Authors: Takuo Minato / Takamasa Teramoto / Naruhiko Adachi / Nguyen Khac Hung / Kaho Yamada / Masato Kawasaki / Masato Akutsu / Toshio Moriya / Toshiya Senda / Seiji Ogo / Yoshimitsu Kakuta / Ki-Seok Yoon / Abstract: C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to ...C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to photosystems I and II. X-ray crystallographic and electron microscopy (EM) analyses have revealed the structure of CPC to be a closed toroidal hexamer by assembling two trimers. In this study, the structural characterization of non-conventional octameric CPC is reported for the first time. Analyses of the crystal and cryogenic EM structures of the native CPC from filamentous thermophilic cyanobacterium Thermoleptolyngbya sp. O-77 unexpectedly illustrated the coexistence of conventional hexamer and novel octamer. In addition, an unusual dimeric state, observed via analytical ultracentrifugation, was postulated to be a key intermediate structure in the assemble of the previously unobserved octamer. These observations provide new insights into the assembly processes of CPCs and the mechanism of energy transfer in the light-harvesting complexes. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7efv.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7efv.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 7efv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/7efv ftp://data.pdbj.org/pub/pdb/validation_reports/ef/7efv | HTTPS FTP |
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-Related structure data
Related structure data | 7efwC 7eh7C 7eh8C 1i7yS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 17560.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. O-77 (bacteria) / References: UniProt: A0A0X8WU90 #2: Protein | Mass: 18097.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. O-77 (bacteria) / References: UniProt: A0A0X8WUE0 #3: Chemical | ChemComp-CYC / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.71 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1.6 M sodium chloride, 8% polyethylene glycol 6,000, 20% glycero |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→49.03 Å / Num. obs: 26620 / % possible obs: 100 % / Redundancy: 61.6 % / CC1/2: 0.998 / Rrim(I) all: 0.378 / Net I/σ(I): 11.39 |
Reflection shell | Resolution: 2.77→2.93 Å / Redundancy: 61.7 % / Num. unique obs: 4259 / CC1/2: 0.557 / Rrim(I) all: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I7Y Resolution: 2.77→49.03 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.77→49.03 Å
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Refine LS restraints |
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LS refinement shell |
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