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Yorodumi- PDB-6lu1: Cyanobacterial PSI Monomer from T. elongatus by Single Particle C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lu1 | |||||||||
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Title | Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A Resolution | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / monomer / complex / photosystem / photosynthesis | |||||||||
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 / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) Thermosynechococcus elongatus (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Kurisu, G. / Coruh, O. / Tanaka, H. / Gerle, C. / Kawamoto, A. / Kato, T. / Namba, K. / Nowaczyk, M.M. / Rogner, M. / Misumi, Y. ...Kurisu, G. / Coruh, O. / Tanaka, H. / Gerle, C. / Kawamoto, A. / Kato, T. / Namba, K. / Nowaczyk, M.M. / Rogner, M. / Misumi, Y. / Frank, A. / Eithar, E.M. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Commun Biol / Year: 2021 Title: Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Authors: Orkun Çoruh / Anna Frank / Hideaki Tanaka / Akihiro Kawamoto / Eithar El-Mohsnawy / Takayuki Kato / Keiichi Namba / Christoph Gerle / Marc M Nowaczyk / Genji Kurisu / Abstract: A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric ...A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700. | |||||||||
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 | 6lu1.cif.gz | 493.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lu1.ent.gz | 417 KB | Display | PDB format |
PDBx/mmJSON format | 6lu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lu1_validation.pdf.gz | 5.1 MB | Display | wwPDB validaton report |
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Full document | 6lu1_full_validation.pdf.gz | 5.3 MB | Display | |
Data in XML | 6lu1_validation.xml.gz | 65.7 KB | Display | |
Data in CIF | 6lu1_validation.cif.gz | 88 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/6lu1 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6lu1 | HTTPS FTP |
-Related structure data
Related structure data | 0977MC 7bw2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10352 (Title: 3.2 Å resolution structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus BP-1 by single particle cryo-EM with a 200 kV CRYO ARM electron microscope Data size: 226.1 Data #1: Raw, non aligned micrograph movies in compressed TIFF format. [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 83267.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) Strain: BP-1 / 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) Strain: BP-1 / References: UniProt: P0A407, photosystem I |
-Protein , 1 types, 1 molecules C
#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) Strain: BP-1 / References: UniProt: P0A415, photosystem I |
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-Photosystem I reaction center subunit ... , 7 types, 7 molecules DEFIJLM
#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) Strain: BP-1 / References: UniProt: P0A420 |
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#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) Strain: BP-1 / References: UniProt: P0A423 |
#6: Protein | Mass: 17716.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) Strain: BP-1 / References: UniProt: P0A401 |
#7: Protein/peptide | Mass: 4297.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) Strain: BP-1 / References: UniProt: P0A427 |
#8: Protein/peptide | Mass: 4770.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) Strain: BP-1 / References: UniProt: P0A429 |
#9: Protein | Mass: 16261.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DGB4 |
#10: 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) Strain: BP-1 / References: UniProt: P0A403 |
-Non-polymers , 7 types, 121 molecules
#11: Chemical | ChemComp-CLA / #12: Chemical | #13: Chemical | ChemComp-BCR / #14: Chemical | #15: Chemical | #16: Chemical | ChemComp-LMG / | #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: Cyanobacterial PSI Monomer from T. elongatus / Type: COMPLEX Details: The monomers in this sample are generated by the monomerization of trimers of PSI during the purification process. Entity ID: #1-#10 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 350 kDa/nm / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Thermosynechococcus elongatus BP-1 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was monodisperse. | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 200 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Calibrated magnification: 56497 X / Calibrated defocus min: 500 nm / Calibrated defocus max: 3500 nm / Cs: 1.4 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL / Temperature (max): 100.4 K / Temperature (min): 100.4 K |
Image recording | Average exposure time: 12 sec. / Electron dose: 1.34 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 60 / Used frames/image: 1-60 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 182018 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46105 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 45 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1JB0 Accession code: 1JB0 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.2 Å | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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