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- PDB-8eqm: Structure of a dimeric photosystem II complex acclimated to far-r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8eqm | ||||||||||||
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Title | Structure of a dimeric photosystem II complex acclimated to far-red light | ||||||||||||
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![]() | PHOTOSYNTHESIS / Far-red / photosystem II / cyanobacteria / chlorophyll | ||||||||||||
Function / homology | ![]() cytochrome c-heme linkage / photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / photosystem II / extrinsic component of membrane ...cytochrome c-heme linkage / photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / photosystem II / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||
![]() | Gisriel, C.J. / Shen, G. / Flesher, D.A. / Kurashov, V. / Golbeck, J.H. / Brudvig, G.W. / Amin, M. / Bryant, D.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light. Authors: Christopher J Gisriel / Gaozhong Shen / David A Flesher / Vasily Kurashov / John H Golbeck / Gary W Brudvig / Muhamed Amin / Donald A Bryant / ![]() ![]() Abstract: Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which ...Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400-700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700-800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL-PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL. | ||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 948.9 KB | Display | ![]() |
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PDB format | ![]() | 805.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.3 MB | Display | ![]() |
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Full document | ![]() | 6.8 MB | Display | |
Data in XML | ![]() | 215.6 KB | Display | |
Data in CIF | ![]() | 285.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28539MC M: map data used to model this data 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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Components
-Photosystem II ... , 13 types, 26 molecules AaBbCcDdHhIiKkLlMmOoTtUuXx
#1: Protein | Mass: 39958.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 56440.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 52375.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 39596.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 7247.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein/peptide | Mass: 4229.917 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein/peptide | Mass: 5069.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein/peptide | Mass: 4566.261 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein/peptide | Mass: 3980.772 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 29319.096 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein/peptide | Mass: 3606.362 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 17325.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein/peptide | Mass: 4273.182 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9136.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein/peptide | Mass: 5023.960 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein , 1 types, 2 molecules Vv
#15: Protein | Mass: 18814.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 2 types, 8 molecules ![](data/chem/img/DGD.gif)
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#28: Sugar | ChemComp-DGD / #33: Sugar | |
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-Non-polymers , 16 types, 714 molecules ![](data/chem/img/OEX.gif)
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![](data/chem/img/CL.gif)
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![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/CL7.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HEM.gif)
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![](data/chem/img/HOH.gif)
#17: Chemical | #18: Chemical | #19: Chemical | ChemComp-CL / #20: Chemical | ChemComp-CLA / #21: Chemical | ChemComp-PHO / #22: Chemical | ChemComp-BCR / #23: Chemical | ChemComp-SQD / #24: Chemical | ChemComp-PL9 / #25: Chemical | #26: Chemical | ChemComp-LHG / #27: Chemical | ChemComp-F6C / #29: Chemical | #30: Chemical | ChemComp-LMG / #31: Chemical | ChemComp-HEM / #32: Chemical | #34: Water | ChemComp-HOH / | |
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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 |
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Sample preparation
Component | Name: Far-red light-acclimated photosystem II / Type: COMPLEX / Entity ID: #3, #1-#2, #4-#16 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 6.5 |
Specimen | Conc.: 0.65 mg/ml / 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 defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 41.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90191 / Symmetry type: POINT |