[English] 日本語
Yorodumi- PDB-7qco: The structure of Photosystem I tetramer from Chroococcidiopsis TS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qco | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of Photosystem I tetramer from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium | ||||||||||||
Components |
| ||||||||||||
Keywords | PHOTOSYNTHESIS / Photosystem I / cyanobacterium Chroococcidiopsis sp. TS-821 | ||||||||||||
Function / homology | Function and homology information 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 / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chroococcidiopsis sp. TS-821 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Semchonok, D.A. / Mondal, J. / Cooper, J.C. / Schlum, K. / Li, M. / Amin, M. / Sorzano, C.O.S. / Ramirez-Aportela, E. / Kastritis, P.L. / Boekema, E.J. ...Semchonok, D.A. / Mondal, J. / Cooper, J.C. / Schlum, K. / Li, M. / Amin, M. / Sorzano, C.O.S. / Ramirez-Aportela, E. / Kastritis, P.L. / Boekema, E.J. / Guskov, A. / Bruce, B.D. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Plant Commun / Year: 2022 Title: Cryo-EM structure of a tetrameric photosystem I from TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium. Authors: Dmitry A Semchonok / Jyotirmoy Mondal / Connor J Cooper / Katrina Schlum / Meng Li / Muhamed Amin / Carlos O S Sorzano / Erney Ramírez-Aportela / Panagiotis L Kastritis / Egbert J Boekema / ...Authors: Dmitry A Semchonok / Jyotirmoy Mondal / Connor J Cooper / Katrina Schlum / Meng Li / Muhamed Amin / Carlos O S Sorzano / Erney Ramírez-Aportela / Panagiotis L Kastritis / Egbert J Boekema / Albert Guskov / Barry D Bruce / Abstract: Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric ...Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms. #1: Journal: Plant Commun / Year: 2022 Title: Cryo-EM structure of a tetrameric photosystem I from TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium. Authors: Dmitry A Semchonok / Jyotirmoy Mondal / Connor J Cooper / Katrina Schlum / Meng Li / Muhamed Amin / Carlos O S Sorzano / Erney Ramírez-Aportela / Panagiotis L Kastritis / Egbert J Boekema / ...Authors: Dmitry A Semchonok / Jyotirmoy Mondal / Connor J Cooper / Katrina Schlum / Meng Li / Muhamed Amin / Carlos O S Sorzano / Erney Ramírez-Aportela / Panagiotis L Kastritis / Egbert J Boekema / Albert Guskov / Barry D Bruce / Abstract: Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric ...Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qco.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qco.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 7qco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qco_validation.pdf.gz | 30.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qco_full_validation.pdf.gz | 31.2 MB | Display | |
Data in XML | 7qco_validation.xml.gz | 340.4 KB | Display | |
Data in CIF | 7qco_validation.cif.gz | 431.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/7qco ftp://data.pdbj.org/pub/pdb/validation_reports/qc/7qco | HTTPS FTP |
-Related structure data
Related structure data | 13898MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 8 molecules AEeaBGgb
#1: Protein | Mass: 83352.641 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VGM5, photosystem I #2: Protein | Mass: 82656.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VGS2, photosystem I |
---|
-Protein , 1 types, 4 molecules CHhc
#3: Protein | Mass: 8939.309 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VD54, photosystem I |
---|
-Photosystem I reaction center subunit ... , 8 types, 32 molecules DNndVWvwFOofIPpiJQqjKRrkLSslMTtm
#4: Protein | Mass: 18520.025 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VI21 #5: Protein | Mass: 13551.099 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VHU0 #6: Protein | Mass: 18131.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VDZ1 #7: Protein/peptide | Mass: 4194.028 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VDT4 #8: Protein/peptide | Mass: 5760.832 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: BCR is not the part of the protein sequence / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: V5JYA2 #9: Protein | Mass: 9753.610 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: CLA is not the part of the protein sequence / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6V467 #10: Protein | Mass: 18503.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: V5JYE0 #11: Protein/peptide | Mass: 3382.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6V6A8 |
---|
-Non-polymers , 5 types, 462 molecules
#12: Chemical | ChemComp-LHG / #13: Chemical | ChemComp-CLA / #14: Chemical | ChemComp-PQN / #15: Chemical | ChemComp-BCR / #16: Chemical | ChemComp-SF4 / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Photosystem I / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 1.6 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Chroococcidiopsis sp. TS-821 (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 0.32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 12 sec. / Electron dose: 4.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4845 |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 24 |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3243 Details: 325648 particles were selected from 4845 micrograph movies | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66130 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1JB0 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|