+Open data
-Basic information
Entry | Database: PDB / ID: 6jeo | ||||||
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Title | Structure of PSI tetramer from Anabaena | ||||||
Components | (Photosystem I ...) x 12 | ||||||
Keywords | PHOTOSYNTHESIS / Photosystem | ||||||
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 | Nostoc sp. (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Kato, K. / Nagao, R. / Shen, J.R. / Miyazaki, N. / Akita, F. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy. Authors: Koji Kato / Ryo Nagao / Tian-Yi Jiang / Yoshifumi Ueno / Makio Yokono / Siu Kit Chan / Mai Watanabe / Masahiko Ikeuchi / Jian-Ren Shen / Seiji Akimoto / Naoyuki Miyazaki / Fusamichi Akita / Abstract: Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a ...Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations. | ||||||
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 | 6jeo.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6jeo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6jeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jeo_validation.pdf.gz | 22.5 MB | Display | wwPDB validaton report |
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Full document | 6jeo_full_validation.pdf.gz | 23.6 MB | Display | |
Data in XML | 6jeo_validation.xml.gz | 393.2 KB | Display | |
Data in CIF | 6jeo_validation.cif.gz | 510.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/6jeo ftp://data.pdbj.org/pub/pdb/validation_reports/je/6jeo | HTTPS FTP |
-Related structure data
Related structure data | 9807MC 9877C 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, 48 molecules aAbAcAdAaBbBcBdBaCbCcCdCaDbDcDdDaEbEcEdEaFbFcFdFaIbIcIdIaJbJ...
#1: Protein | Mass: 83289.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58576, photosystem I #2: Protein | Mass: 83457.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58565, photosystem I #3: Protein | Mass: 8825.206 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P0A410, photosystem I #4: Protein | Mass: 15176.240 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58573 #5: Protein | Mass: 7897.051 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58575 #6: Protein | Mass: 17850.568 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58564 #7: Protein/peptide | Mass: 5066.925 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58560 #8: Protein/peptide | Mass: 5499.422 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58568 #9: Protein | Mass: 8852.457 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58583 #10: Protein | Mass: 18130.725 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58577 #11: Protein/peptide | Mass: 4424.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YNB0 #12: Protein/peptide | Mass: 4872.792 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58566 |
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-Non-polymers , 7 types, 504 molecules
#13: Chemical | ChemComp-CL0 / #14: Chemical | ChemComp-CLA / #15: Chemical | ChemComp-PQN / #16: Chemical | ChemComp-SF4 / #17: Chemical | ChemComp-BCR / #18: Chemical | ChemComp-LHG / #19: Chemical | ChemComp-LMG / |
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-Details
Has ligand of interest | N |
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Sequence details | The sequence was based on sequence reference BAB76356.1. The associated accession in UNIPROT, ...The sequence was based on sequence reference BAB76356.1. The associated accession in UNIPROT, Q8YNB0 (PSAM_NOSS1), differs from NCBI with translation N-terminally shortened. |
-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: PSI tetramer / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL | ||||||||||||
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Molecular weight | Value: 1.44 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Nostoc sp. PCC 7120 (bacteria) | ||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.014 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: (1.14_3260: phenix.real_space_refine) / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111400 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1JB0 |