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- PDB-8h2u: X-ray Structure of photosystem I-LHCI super complex from Chlamydo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h2u | |||||||||
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Title | X-ray Structure of photosystem I-LHCI super complex from Chlamydomonas reinhardtii. | |||||||||
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![]() | PHOTOSYNTHESIS / Photosystem I / light-harvesting chlorophyll protein complex I | |||||||||
Function / homology | ![]() chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus ...chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tanaka, H. / Kubota-Kawai, H. / Misumi, Y. / Kurisu, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin. Authors: Christoph Gerle / Yuko Misumi / Akihiro Kawamoto / Hideaki Tanaka / Hisako Kubota-Kawai / Ryutaro Tokutsu / Eunchul Kim / Dror Chorev / Kazuhiro Abe / Carol V Robinson / Kaoru Mitsuoka / Jun ...Authors: Christoph Gerle / Yuko Misumi / Akihiro Kawamoto / Hideaki Tanaka / Hisako Kubota-Kawai / Ryutaro Tokutsu / Eunchul Kim / Dror Chorev / Kazuhiro Abe / Carol V Robinson / Kaoru Mitsuoka / Jun Minagawa / Genji Kurisu / ![]() ![]() Abstract: Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural ...Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural characterization of soluble binding partners is less advanced. Here, we used X-ray crystallography and single particle cryo-EM to investigate three structures of the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. An X-ray structure demonstrates the absence of six chlorophylls from the luminal side of the LHCI belts, suggesting these pigments were either physically absent or less stably associated with the complex, potentially influencing excitation transfer significantly. CryoEM revealed extra densities on luminal and stromal sides of the supercomplex, situated in the vicinity of the electron transfer sites. These densities disappeared after the binding of oxidized ferredoxin to PSI-LHCI. Based on these structures, we propose the existence of a PSI-LHCI resting state with a reduced active chlorophyll content, electron donors docked in waiting positions and regulatory binding partners positioned at the electron acceptor site. The resting state PSI-LHCI supercomplex would be recruited to its active form by the availability of oxidized ferredoxin. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 940 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 65 MB | Display | ![]() |
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Full document | ![]() | 65.5 MB | Display | |
Data in XML | ![]() | 235.4 KB | Display | |
Data in CIF | ![]() | 279.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wyiC ![]() 7wznC ![]() 4xk8S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 83239.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 82184.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 3 types, 3 molecules CL3
#3: Protein | Mass: 8869.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#12: Protein | Mass: 20300.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 32629.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE GENEBANK ACCESSION NUMBER IS 6IJJ_3 for Lhca3. (www.ncbi.nlm.nih.gov/protein/6IJJ_3) Source: (natural) ![]() ![]() |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFGHIJK
#4: Protein | Mass: 21372.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 10786.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 24088.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 13236.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 14173.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 10586.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein/peptide | Mass: 4750.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 11214.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Chlorophyll a-b binding protein, ... , 6 types, 7 molecules 0187465
#13: Protein | Mass: 23923.205 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | | Mass: 25948.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | | Mass: 26249.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | | Mass: 28729.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | | Mass: 27812.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | | Mass: 28257.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/DGD.gif)
![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#25: Sugar | #26: Sugar | |
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-Non-polymers , 9 types, 274 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/XAT.gif)
#20: Chemical | ChemComp-CLA / #21: Chemical | #22: Chemical | #23: Chemical | ChemComp-LHG / #24: Chemical | ChemComp-BCR / #27: Chemical | ChemComp-LMG / #28: Chemical | ChemComp-LUT / ( #29: Chemical | ChemComp-CHL / #30: Chemical | ChemComp-XAT / ( |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 50 mM Tris-HCl (pH 7.0), 50 mM Li2SO4 and 4.5-7.0 % (w/v) polyethylene glycol (PEG) 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→47.74 Å / Num. obs: 123685 / % possible obs: 98.9 % / Redundancy: 5.7 % / CC1/2: 0.97 / Rmerge(I) obs: 0.145 / Net I/σ(I): 11.98 |
Reflection shell | Resolution: 3.25→3.32 Å / Rmerge(I) obs: 2.299 / Num. unique obs: 9090 / CC1/2: 0.552 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XK8 Resolution: 3.4→47.74 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.4→47.74 Å
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LS refinement shell | Resolution: 3.4→3.49 Å
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