+Open data
-Basic information
Entry | Database: PDB / ID: 6pnj | |||||||||||||||
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Title | Structure of Photosystem I Acclimated to Far-red Light | |||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / trimeric alpha helical complex | |||||||||||||||
Function / homology | Function and homology information thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Fischerella thermalis PCC 7521 (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||||||||
Authors | Gisriel, C.J. / Shen, G. / Kurashov, V. / Ho, M. / Zhang, S. / Williams, D. / Golbeck, J.H. / Fromme, P. / Bryant, D.A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Sci Adv / Year: 2020 Title: The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis. Authors: Christopher Gisriel / Gaozhong Shen / Vasily Kurashov / Ming-Yang Ho / Shangji Zhang / Dewight Williams / John H Golbeck / Petra Fromme / Donald A Bryant / Abstract: Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria ...Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria overcome this challenge by expressing paralogous photosynthetic proteins and by synthesizing and incorporating ~8% chlorophyll f into their Photosystem I (PSI) complexes, enabling them to grow under far-red light (FRL). We solved the structure of FRL-acclimated PSI from the cyanobacterium PCC 7521 by single-particle, cryo-electron microscopy to understand its structural and functional differences. Four binding sites occupied by chlorophyll f are proposed. Subtle structural changes enable FRL-adapted PSI to extend light utilization for oxygenic photosynthesis to nearly 800 nm. This structure provides a platform for understanding FRL-driven photosynthesis and illustrates the robustness of adaptive and acclimation mechanisms in nature. | |||||||||||||||
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 | 6pnj.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6pnj.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6pnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/6pnj ftp://data.pdbj.org/pub/pdb/validation_reports/pn/6pnj | HTTPS FTP |
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-Related structure data
Related structure data | 20397MC 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 ... , 11 types, 33 molecules AGaBHbCNcDOdEPeFQfIRiJSjKTkLUl...
#1: Protein | Mass: 87627.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FME9, photosystem I #2: Protein | Mass: 83450.969 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) References: UniProt: A0A2N6KXB6, UniProt: G6FMF0*PLUS, photosystem I #3: Protein | Mass: 8853.221 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FW50, photosystem I #4: Protein | Mass: 17776.348 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FW99 #5: Protein | Mass: 8070.138 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FQU3 #6: Protein | Mass: 17788.021 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FMD3 #7: Protein | Mass: 7735.956 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: A0A2N6MR25, UniProt: A0A2N6M8S7*PLUS #8: Protein/peptide | Mass: 5435.492 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FMD2 #9: Protein/peptide | Mass: 3615.425 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FV28 #10: Protein | Mass: 18543.229 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: A0A2N6M3Z9, UniProt: G6FMF1*PLUS #11: Protein/peptide | Mass: 3471.115 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FWT6 |
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-Protein / Sugars , 2 types, 9 molecules WXx
#12: Protein | Mass: 11132.814 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FSH2 #21: Sugar | ChemComp-LMT / |
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-Non-polymers , 9 types, 366 molecules
#13: Chemical | #14: Chemical | ChemComp-CLA / #15: Chemical | ChemComp-F6C / Mass: 905.457 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H68MgN4O6 #16: Chemical | ChemComp-PQN / #17: Chemical | ChemComp-SF4 / #18: Chemical | ChemComp-BCR / #19: Chemical | ChemComp-LHG / #20: Chemical | ChemComp-LMG / #22: 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: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Photosystem I from far-red light-adapted Fischerella thermalis PCC 7521 Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL | ||||||||||||||||||||
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Source (natural) | Organism: Fischerella thermalis PCC 7521 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 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 FIELDBright-field microscopy |
Image recording | Electron dose: 1.5252 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178666 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.2→424 Å / SU ML: 0.9762 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 44.0042 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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