+Open data
-Basic information
Entry | Database: PDB / ID: 7dr2 | ||||||
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Title | Structure of GraFix PSI tetramer from Cyanophora paradoxa | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information cyanelle thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding ...cyanelle thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Cyanophora paradoxa (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Kato, K. / Nagao, R. / Akita, F. / Miyazaki, N. / Shen, J.R. | ||||||
Citation | Journal: Biorxiv / Year: 2022 Title: Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes Authors: Kato, K. / Nagao, R. / Ueno, Y. / Yokono, M. / Suzuki, T. / Jiang, T.Y. / Dohmae, N. / Akita, F. / Akimoto, S. / Miyazaki, N. / Shen, J.R. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7dr2.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7dr2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7dr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/7dr2 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/7dr2 | HTTPS FTP |
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-Related structure data
Related structure data | 30823MC 7dr0C 7dr1C 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
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 8 molecules aAbAcAdAaBbBcBdB
#1: Protein | Mass: 83397.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: A0A097PBL3, photosystem I #2: Protein | Mass: 82316.312 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48113, photosystem I |
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-Protein , 1 types, 4 molecules aCbCcCdC
#3: Protein | Mass: 8850.221 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P31173, photosystem I |
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-Photosystem I reaction center subunit ... , 8 types, 30 molecules aDbDcDdDaEbEcEdEaFbFcFdFaIbIcIdIaJbJcJdJaKcKaLbLcLdLaMbMcMdM
#4: Protein | Mass: 23693.258 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: Q9T4W8 #5: Protein | Mass: 8058.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48114 #6: Protein | Mass: 20697.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48115 #7: Protein/peptide | Mass: 3772.620 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48116 #8: Protein/peptide | Mass: 4483.274 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48117 #9: Protein | Mass: 15704.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) #10: Protein | Mass: 15376.591 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) #11: Protein/peptide | Mass: 3334.065 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48185 |
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-Non-polymers , 7 types, 438 molecules
#12: Chemical | ChemComp-CL0 / #13: Chemical | ChemComp-CLA / #14: Chemical | ChemComp-PQN / #15: Chemical | ChemComp-BCR / #16: Chemical | ChemComp-LHG / #17: Chemical | ChemComp-SF4 / #18: Chemical | ChemComp-LMG / |
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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 |
-Sample preparation
Component | Name: PSI tetramer / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL | ||||||||||||
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Molecular weight | Value: 1.4 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Cyanophora paradoxa (eukaryote) | ||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.048 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 723316 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40679 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient |