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Yorodumi- PDB-7ezx: Structure of the phycobilisome from the red alga Porphyridium pur... -
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Basic information
| Entry | Database: PDB / ID: 7ezx | |||||||||
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| Title | Structure of the phycobilisome from the red alga Porphyridium purpureum in Middle Light | |||||||||
 Components |
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 Keywords | PHOTOSYNTHESIS / light-harvesting complex | |||||||||
| Function / homology |  Function and homology informationphycobilisome / chloroplast thylakoid membrane / photosynthesis / cell adhesion molecule binding / extracellular matrix organization / extracellular matrix / macroautophagy / cell adhesion / lyase activity / extracellular space Similarity search - Function | |||||||||
| Biological species |  Porphyridium purpureum (eukaryote) | |||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
 Authors | Ma, J.F. / Sui, S.-F. | |||||||||
| Funding support |  China, 2items
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 Citation | Journal: Commun Biol / Year: 2023 Title: The structural basis for light acclimation in phycobilisome light harvesting systems systems in Porphyridium purpureum Authors: Dodson, E.J. / Ma, J. / Suissa Szlejf, M. / Maroudas-Sklare, N. / Paltiel, Y. / Adir, N. / Sun, S. / Sui, S.F. / Keren, N. | |||||||||
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Structure visualization
| Structure viewer | Molecule: MolmilJmol/JSmol |
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Downloads & links
-Download
| PDBx/mmCIF format | 7ezx.cif.gz | 19.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb7ezx.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 7ezx.json.gz | Tree view | PDBx/mmJSON format | |
| Others |  Other downloads |
-Validation report
| Summary document | 7ezx_validation.pdf.gz | 150.7 MB | Display | wwPDB validaton report |
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| Full document | 7ezx_full_validation.pdf.gz | 135.7 MB | Display | |
| Data in XML | 7ezx_validation.xml.gz | 3.6 MB | Display | |
| Data in CIF | 7ezx_validation.cif.gz | 4.1 MB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/7ezxftp://data.pdbj.org/pub/pdb/validation_reports/ez/7ezx | HTTPS FTP |
-Related structure data
| Related structure data |  31393MC 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
-Phycobilisome ... , 10 types, 28 molecules X1X7X9XFXIXKB1B7B9BFBIBKe2eRO3OOd4dDbBbMMCMEzJzLXPzPYP1P
| #1: Protein | Mass: 39743.625 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YM59#3: Protein | Mass: 26996.689 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RZ90#8: Protein | Mass: 32886.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z7F4#9: Protein | Mass: 43968.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YMI8#10: Protein | Mass: 37175.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z162#15: Protein | Mass: 53601.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX63#18: Protein | Mass: 34958.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z323#19: Protein | Mass: 55146.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YI31#24: Protein | Mass: 14108.206 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YVZ2#25: 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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-R-phycoerythrin gamma chain, ... , 4 types, 20 molecules A1A7A9AFAIAKMAMGMNMQABwJxJwLxLAMBByJyLBM
| #2: Protein | Mass: 31792.982 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX19#14: Protein | Mass: 36924.992 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YNU6#16: Protein | Mass: 29453.639 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YZM7#17: Protein | Mass: 31358.787 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YZH3 |
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-C-phycocyanin ... , 2 types, 72 molecules C1E1G1I1K1M1C7E7G7I7K7M7C9E9G9I9K9M9CFEFGFIFKFMFCIEIGIIIKIMI...
| #4: Protein | Mass: 17478.664 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RYI4#5: 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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-Protein , 6 types, 488 molecules O1Q1S1U1W1Z1b1d1f1h1j1l1M2O2Q2S2U2W2A3C3E3G3I3K3B4D4F4H4J4L4...
| #6: Protein | Mass: 17824.029 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: E2IH77#7: Protein | Mass: 18584.182 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: P11393#11: Protein | Mass: 36402.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX67#12: Protein | Mass: 31172.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YJY8#26: Protein | Mass: 16915.260 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YTV6#27: Protein | Mass: 30272.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z2M2 |
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-FAS1 domain-containing ... , 2 types, 4 molecules k6kHbP4P
| #13: Protein | Mass: 31332.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z027#28: Protein | Mass: 26620.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4ZA95 |
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-Allophycocyanin ... , 4 types, 46 molecules APCPEPGPJPKPNPPPRPTPcPePgPiPlPmPpPrPtPvPDPFPBPHPIPLPMPOPQPSP...
| #20: Protein | Mass: 17639.123 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0RYM0#21: Protein | Mass: 17415.797 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0S279#22: Protein | Mass: 18126.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: W0S1U6#23: 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 , 4 types, 1462 molecules 
| #29: Chemical | ChemComp-PEB /  Mass: 588.694 Da / Num. of mol.: 1298 / Source method: obtained synthetically / Formula: C33H40N4O6#30: Chemical | ChemComp-PUB /  Mass: 590.710 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C33H42N4O6 / Feature type: SUBJECT OF INVESTIGATION#31: Chemical | ChemComp-CYC /  Mass: 588.694 Da / Num. of mol.: 120 / Source method: obtained synthetically / Formula: C33H40N4O6#32: Chemical | ChemComp-PMS /  Mass: 172.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8O3S |
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-Details
| Has ligand of interest | Y |
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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: phycobilisome / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL | |||||||||||||||
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| Molecular weight | Value: 14700 kDa/nm / Experimental value: NO | |||||||||||||||
| Source (natural) | Organism: Porphyridium purpureum (eukaryote) | |||||||||||||||
| Buffer solution | pH: 7 | |||||||||||||||
| Buffer component |
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| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
| Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon | |||||||||||||||
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 18 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: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 130000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1300 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 2300 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K |
| Image recording | Average exposure time: 8.2 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6438 |
| EM imaging optics | Energyfilter name: GIF Quantum ER |
| Image scans | Width: 4096 / Height: 4096 / Movie frames/image: 32 / Used frames/image: 1-32 |
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Processing
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| CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 315046 | ||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87399 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
| Atomic model building | B value: 62.05 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: 0,99 | ||||||||||||||||||||||||||||||||
| Atomic model building | PDB-ID: 6KGX Accession code: 6KGX / Source name: PDB / Type: experimental model |
