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- PDB-7blx: Photosystem I of a temperature sensitive mutant Chlamydomonas rei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7blx | |||||||||
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Title | Photosystem I of a temperature sensitive mutant Chlamydomonas reinhardtii | |||||||||
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![]() | PHOTOSYNTHESIS / chlamydomonas / photosystem I / temperature sensitive / water molecules | |||||||||
Function / homology | ![]() plastoglobule / 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 ...plastoglobule / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
![]() | Caspy, I. / Nelson, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Dimeric and high-resolution structures of Chlamydomonas Photosystem I from a temperature-sensitive Photosystem II mutant. Authors: Ido Caspy / Tom Schwartz / Vinzenz Bayro-Kaiser / Mariia Fadeeva / Amit Kessel / Nir Ben-Tal / Nathan Nelson / ![]() Abstract: Water molecules play a pivotal functional role in photosynthesis, primarily as the substrate for Photosystem II (PSII). However, their importance and contribution to Photosystem I (PSI) activity ...Water molecules play a pivotal functional role in photosynthesis, primarily as the substrate for Photosystem II (PSII). However, their importance and contribution to Photosystem I (PSI) activity remains obscure. Using a high-resolution cryogenic electron microscopy (cryo-EM) PSI structure from a Chlamydomonas reinhardtii temperature-sensitive photoautotrophic PSII mutant (TSP4), a conserved network of water molecules - dating back to cyanobacteria - was uncovered, mainly in the vicinity of the electron transport chain (ETC). The high-resolution structure illustrated that the water molecules served as a ligand in every chlorophyll that was missing a fifth magnesium coordination in the PSI core and in the light-harvesting complexes (LHC). The asymmetric distribution of the water molecules near the ETC branches modulated their electrostatic landscape, distinctly in the space between the quinones and FX. The data also disclosed the first observation of eukaryotic PSI oligomerisation through a low-resolution PSI dimer that was comprised of PSI-10LHC and PSI-8LHC. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 958.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 13.6 MB | Display | ![]() |
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Full document | ![]() | 14.7 MB | Display | |
Data in XML | ![]() | 287.8 KB | Display | |
Data in CIF | ![]() | 341.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12227MC ![]() 7bgiC ![]() 7o01C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 82121.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 81996.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules CL
#3: Protein | Mass: 8738.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#11: Protein | Mass: 12944.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Photosystem I reaction center subunit ... , 7 types, 7 molecules DEFGIJK
#4: Protein | Mass: 16152.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 7021.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 17957.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 9572.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein/peptide | Mass: 3970.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein/peptide | Mass: 4516.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 8146.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Chlorophyll a-b binding protein, ... , 7 types, 8 molecules 1Z378456
#12: Protein | Mass: 20368.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | | Mass: 23689.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | | Mass: 23304.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | | Mass: 23293.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | | Mass: 23018.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | | Mass: 25122.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | | Mass: 24937.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 8 molecules ![](data/chem/img/LMT.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#26: Sugar | ChemComp-LMT / #31: Sugar | ChemComp-DGD / | |
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+Non-polymers , 23 types, 640 molecules ![](data/chem/img/CL0.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/NKP.gif)
![](data/chem/img/OCA.gif)
![](data/chem/img/DAO.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/C7Z.gif)
![](data/chem/img/SPH.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/QTB.gif)
![](data/chem/img/3PH.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/LPX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/NKP.gif)
![](data/chem/img/OCA.gif)
![](data/chem/img/DAO.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/C7Z.gif)
![](data/chem/img/SPH.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/QTB.gif)
![](data/chem/img/3PH.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/LPX.gif)
![](data/chem/img/HOH.gif)
-Details
Has ligand of interest | N |
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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 |
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Sample preparation
Component | Name: Photosystem I of temperature sensitive Chlamydomonas reinhardtii Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Molecular weight | Value: 0.89 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 46.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 12418 |
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Processing
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1208518 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17311 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6JO5 | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.2 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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