+Open data
-Basic information
Entry | Database: PDB / ID: 7vd6 | ||||||
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Title | Structure of S1M1-type FCPII complex from diatom | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Photosystem / PSII | ||||||
Function / homology | Function and homology information light-harvesting complex / photosynthesis, light harvesting / plastid / membrane Similarity search - Function | ||||||
Biological species | Chaetoceros gracilis (Diatom) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Nagao, R. / Kato, K. / Akita, F. / Miyazaki, N. / Shen, J.R. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex Authors: Nagao, R. / Kato, K. / Kumazawa, M. / Ifuku, K. / Yokono, M. / Suzuki, T. / 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 | 7vd6.cif.gz | 527.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vd6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7vd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/7vd6 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/7vd6 | HTTPS FTP |
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-Related structure data
Related structure data | 31906MC 7vd5C 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
-Protein , 7 types, 11 molecules 1113141518121617192021
#1: Protein | Mass: 22098.182 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6 #2: Protein | | Mass: 22162.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #3: Protein | | Mass: 22627.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #4: Protein | | Mass: 22298.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #5: Protein | | Mass: 29014.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #6: Protein | | Mass: 23934.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #7: Protein | | Mass: 21143.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
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-Sugars , 1 types, 1 molecules
#16: Sugar | ChemComp-LMU / |
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-Non-polymers , 9 types, 208 molecules
#8: Chemical | ChemComp-CLA / #9: Chemical | ChemComp-KC1 / #10: Chemical | ChemComp-A86 / ( #11: Chemical | ChemComp-LMG / #12: Chemical | ChemComp-UNL / Num. of mol.: 19 / Source method: obtained synthetically #13: Chemical | ChemComp-DD6 / ( #14: Chemical | #15: Chemical | ChemComp-LHG / #17: Water | ChemComp-HOH / | |
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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: S1M1-type FCPII complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL | ||||||||||||
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Molecular weight | Value: 0.24 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Chaetoceros gracilis (Diatom) | ||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.256 mg/ml / 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: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 FIELDBright-field microscopy |
Image recording | Electron dose: 20 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: 8093924 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 373897 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6J40 |