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Open data
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Basic information
Entry | Database: PDB / ID: 7f4v | ||||||
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Title | Cryo-EM structure of a primordial cyanobacterial photosystem I | ||||||
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![]() | PHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT | ||||||
Function / homology | ![]() thylakoid membrane / photosystem I reaction center / photosystem I / : / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 ...thylakoid membrane / photosystem I reaction center / photosystem I / : / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 Å | ||||||
![]() | Kato, K. / Hamaguchi, T. / Nagao, R. / Kawakami, K. / Yonekura, K. / Shen, J.R. | ||||||
![]() | ![]() Title: Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI Authors: Kato, K. / Hamaguchi, T. / Nagao, R. / Kawakami, K. / Ueno, Y. / Suzuki, T. / Uchida, H. / Murakami, A. / Nakajima, Y. / Yokono, M. / Akimoto, S. / Dohmae, N. / Yonekura, K. / Shen, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 16.9 MB | Display | ![]() |
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Full document | ![]() | 18.4 MB | Display | |
Data in XML | ![]() | 339.9 KB | Display | |
Data in CIF | ![]() | 442.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31455MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules aAbAcAaBbBcB
#1: Protein | Mass: 86505.219 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFT6, photosystem I #2: Protein | Mass: 96166.758 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFT5, photosystem I |
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-Photosystem I reaction center subunit ... , 6 types, 18 molecules aDbDcDaEbEcEaFbFcFaIbIcIaLbLcLaMbMcM
#4: Protein | Mass: 15952.242 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NF26 #5: Protein | Mass: 7468.415 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFW6 #6: Protein | Mass: 19931.127 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NH05 #7: Protein/peptide | Mass: 3853.611 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: P0C029 #9: Protein | Mass: 15806.324 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NIE7 #10: Protein/peptide | Mass: 3212.907 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NHY3 |
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-Protein / Protein/peptide , 2 types, 6 molecules aCbCcCaJbJcJ
#3: Protein | Mass: 8807.170 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NG86, photosystem I #8: Protein/peptide | Mass: 2826.475 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29082 / PCC 7421 |
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-Non-polymers , 8 types, 756 molecules ![](data/chem/img/CL0.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/1L3.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/1L3.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HOH.gif)
#11: Chemical | #12: Chemical | ChemComp-CLA / #13: Chemical | ChemComp-1L3 / #14: Chemical | ChemComp-SF4 / #15: Chemical | ChemComp-BCR / #16: Chemical | ChemComp-LHG / #17: Chemical | #18: 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: PSI trimer / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL | ||||||||||||
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Molecular weight | Value: 1.1 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 1.68 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
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 70.22 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261743 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |