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Yorodumi- PDB-6k61: Cryo-EM structure of the tetrameric photosystem I from a heterocy... -
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-Basic information
Entry | Database: PDB / ID: 6k61 | |||||||||
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Title | Cryo-EM structure of the tetrameric photosystem I from a heterocyst-forming cyanobacterium Anabaena sp. PCC7120 | |||||||||
Components | (Photosystem I ...) x 12 | |||||||||
Keywords | PHOTOSYNTHESIS / Photosystem I / PSI / PCC7120 | |||||||||
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. PCC 7120 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å | |||||||||
Authors | Zheng, L. / Li, Y. / Li, X. / Zhong, Q. / Li, N. / Zhang, K. / Zhang, Y. / Chu, H. / Ma, C. / Li, G. ...Zheng, L. / Li, Y. / Li, X. / Zhong, Q. / Li, N. / Zhang, K. / Zhang, Y. / Chu, H. / Ma, C. / Li, G. / Zhao, J. / Gao, N. | |||||||||
Funding support | 1items
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Citation | Journal: Nat Plants / Year: 2019 Title: Structural and functional insights into the tetrameric photosystem I from heterocyst-forming cyanobacteria. Authors: Lvqin Zheng / Yanbing Li / Xiying Li / Qinglu Zhong / Ningning Li / Kun Zhang / Yuebin Zhang / Huiying Chu / Chengying Ma / Guohui Li / Jindong Zhao / Ning Gao / Abstract: Two large protein-cofactor complexes, photosystem I and photosystem II, are the central components of photosynthesis in the thylakoid membranes. Here, we report the 2.37-Å structure of a tetrameric ...Two large protein-cofactor complexes, photosystem I and photosystem II, are the central components of photosynthesis in the thylakoid membranes. Here, we report the 2.37-Å structure of a tetrameric photosystem I complex from a heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Four photosystem I monomers, organized in a dimer of dimer, form two distinct interfaces that are largely mediated by specifically orientated polar lipids, such as sulfoquinovosyl diacylglycerol. The structure depicts a more closely connected network of chlorophylls across monomer interfaces than those seen in trimeric PSI from thermophilic cyanobacteria, possibly allowing a more efficient energy transfer between monomers. Our physiological data also revealed a functional link of photosystem I oligomerization to cyclic electron flow and thylakoid membrane organization. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6k61.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6k61.ent.gz | 976.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k61_validation.pdf.gz | 11.8 MB | Display | wwPDB validaton report |
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Full document | 6k61_full_validation.pdf.gz | 12.4 MB | Display | |
Data in XML | 6k61_validation.xml.gz | 211.6 KB | Display | |
Data in CIF | 6k61_validation.cif.gz | 277.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/6k61 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k61 | HTTPS FTP |
-Related structure data
Related structure data | 9918MC 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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-Components
-Photosystem I ... , 12 types, 24 molecules AaXxBbCcDdEeFfJjKkIiLlMm
#1: Protein | Mass: 83289.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58576, photosystem I #2: Protein/peptide | Mass: 4872.792 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58566 #3: Protein | Mass: 83457.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58565, photosystem I #4: Protein | Mass: 8825.206 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P0A410, photosystem I #5: Protein | Mass: 15176.240 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58573 #6: Protein | Mass: 7897.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58575 #7: Protein | Mass: 17850.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58564 #8: Protein/peptide | Mass: 5499.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58568 #9: Protein | Mass: 8852.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58583 #10: Protein/peptide | Mass: 5066.925 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58560 #11: Protein | Mass: 18130.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58577 #12: Protein/peptide | Mass: 3538.204 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: Q8YNB0 |
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-Non-polymers , 8 types, 259 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-SQD / #20: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Photosystem I complex of cyanobacterium Anabaena sp. PCC 7120 Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#12 / Source: NATURAL |
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Molecular weight | Value: 1.3 MDa |
Source (natural) | Organism: Nostoc sp. PCC 7120 (bacteria) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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 / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71600 / Symmetry type: POINT |