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Yorodumi- PDB-6tra: Cryo- EM structure of the Thermosynechococcus elongatus photosyst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tra | ||||||||||||
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Title | Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of cytochrome c6 | ||||||||||||
Components | (Photosystem I ...) x 12 | ||||||||||||
Keywords | PHOTOSYNTHESIS / Photosystem I / P700 / Cyanobacteria | ||||||||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity ...photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å | ||||||||||||
Authors | Koelsch, A. / Radon, C. / Baumert, A. / Buerger, J. / Miehlke, T. / Lisdat, F. / Zouni, A. / Wendler, P. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Curr.Opin.Struct.Biol. / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6tra.cif.gz | 572.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tra.ent.gz | 510.2 KB | Display | PDB format |
PDBx/mmJSON format | 6tra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tra_validation.pdf.gz | 7.2 MB | Display | wwPDB validaton report |
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Full document | 6tra_full_validation.pdf.gz | 7.5 MB | Display | |
Data in XML | 6tra_validation.xml.gz | 127.2 KB | Display | |
Data in CIF | 6tra_validation.cif.gz | 167.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/6tra ftp://data.pdbj.org/pub/pdb/validation_reports/tr/6tra | HTTPS FTP |
-Related structure data
Related structure data | 10557MC 6trcC 6trdC 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 ... , 12 types, 12 molecules ABCDEFIJKLMX
#1: Protein | Mass: 83267.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A405, photosystem I |
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#2: Protein | Mass: 83123.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A407, photosystem I |
#3: Protein | Mass: 8809.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A415, photosystem I |
#4: Protein | Mass: 15389.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A420 |
#5: Protein | Mass: 8399.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A423 |
#6: Protein | Mass: 15129.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A401 |
#7: Protein/peptide | Mass: 4325.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A427 |
#8: Protein/peptide | Mass: 4798.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A429 |
#9: Protein | Mass: 8483.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A425 |
#10: Protein | Mass: 16287.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DGB4 |
#11: Protein/peptide | Mass: 3426.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: P0A403 |
#12: Protein/peptide | Mass: 4104.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DKP6 |
-Non-polymers , 9 types, 351 molecules
#13: Chemical | ChemComp-CL0 / | ||||||||||||||
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#14: Chemical | ChemComp-CLA / #15: Chemical | #16: Chemical | ChemComp-BCR / #17: Chemical | ChemComp-LHG / #18: Chemical | #19: Chemical | #20: Chemical | ChemComp-LMG / | #21: Water | ChemComp-HOH / | |
-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: photosystem I / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Thermosynechococcus elongatus BP-1 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Photosystem I was crosslinked with its electron donor cytochrome c6. Crosslinked particles are monodisperse. | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175999 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1JB0 |