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Open data
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Basic information
Entry | Database: PDB / ID: 7vd6 | ||||||
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Title | Structure of S1M1-type FCPII complex from diatom | ||||||
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![]() | ELECTRON TRANSPORT / Photosystem / PSII | ||||||
Function / homology | ![]() light-harvesting complex / photosynthesis, light harvesting in photosystem I / plastid / chlorophyll binding / response to light stimulus / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Nagao, R. / Kato, K. / Akita, F. / Miyazaki, N. / Shen, J.R. | ||||||
Funding support | 1items
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 541.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.2 MB | Display | ![]() |
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Full document | ![]() | 10 MB | Display | |
Data in XML | ![]() | 202 KB | Display | |
Data in CIF | ![]() | 229.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31906MC ![]() 7vd5C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() #2: Protein | | Mass: 22162.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | | Mass: 22627.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | | Mass: 22298.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | | Mass: 29014.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | | Mass: 23934.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | | Mass: 21143.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 1 types, 1 molecules ![](data/chem/img/LMU.gif)
#16: Sugar | ChemComp-LMU / |
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-Non-polymers , 9 types, 208 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/KC1.gif)
![](data/chem/img/A86.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/DD6.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/KC1.gif)
![](data/chem/img/A86.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/DD6.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HOH.gif)
#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 |
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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: ![]() | ||||||||||||
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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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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 Accession code: 6J40 / Source name: PDB / Type: experimental model |