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- PDB-6trd: Cryo- EM structure of the Thermosynechococcus elongatus photosyst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6trd | ||||||||||||
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Title | Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of cytochrome c6 | ||||||||||||
![]() | (Photosystem I ...![]() | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Koelsch, A. / Radon, C. / Baumert, A. / Buerger, J. / Mielke, T. / Lisdat, F. / Zouni, A. / Wendler, P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Current limits of structural biology: The transient interaction between cytochrome c6 and photosystem I Authors: Koelsch, A. / Radon, C. / Golub, M. / Baumert, A. / Burger, J. / Miehlke, T. / Lisdat, F. / Feoktystov, A. / Pieper, J. / Zouni, A. / Wendler, P. | ||||||||||||
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 | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 15.5 MB | Display | ![]() |
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Full document | ![]() | 16.2 MB | Display | |
Data in XML | ![]() | 307.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10559MC ![]() 6traC ![]() 6trcC 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
-Photosystem I ... , 12 types, 36 molecules Aa1Bb2Cc3Dd4Ee5Ff6Ii7Jj8Kk9Ll0...
#1: Protein | ![]() Mass: 83267.773 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A405, ![]() #2: Protein | ![]() Mass: 83123.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A407, ![]() #3: Protein | ![]() Mass: 8809.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A415, ![]() #4: Protein | ![]() Mass: 15389.494 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A420 #5: Protein | ![]() Mass: 8399.485 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A423 #6: Protein | ![]() Mass: 15129.358 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A401 #7: Protein/peptide | ![]() Mass: 4325.245 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A427 #8: Protein/peptide | ![]() Mass: 4798.708 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A429 #9: Protein | ![]() Mass: 8483.983 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A425 #10: Protein | ![]() Mass: 16287.765 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q8DGB4 #11: Protein/peptide | ![]() Mass: 3426.115 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A403 #12: Protein/peptide | ![]() Mass: 4104.939 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q8DKP6 |
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-Non-polymers , 9 types, 453 molecules 
















#13: Chemical | ![]() #14: Chemical | ChemComp-CLA / ![]() #15: Chemical | ChemComp-PQN / ![]() #16: Chemical | ChemComp-SF4 / ![]() #17: Chemical | ChemComp-BCR / ![]() #18: Chemical | ChemComp-LHG / ![]() #19: Chemical | ChemComp-CA / #20: Chemical | #21: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: photosystem I![]() | ||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() Details: Photosystem I was crosslinked with its electron donor cytochrome c6. Crosslinked particles are monodisperse. | ||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 32 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction![]() | Details: CTFFIND4 was used to estimate contrast transfer function parameters. CTF correction was done in Relion 3.0. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175999 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1JB0 |