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Yorodumi- PDB-7sa3: Structure of a monomeric photosystem II core complex from a cyano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sa3 | ||||||||||||
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Title | Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem II / far-red light photoacclimation / chlorophyll f / chlorophyll d / bicarbonate / photoactivation / cyanobacteria | ||||||||||||
Function / homology | Function and homology information oxygen evolving activity / photosystem II / photosystem II reaction center / : / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity ...oxygen evolving activity / photosystem II / photosystem II reaction center / : / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / membrane => GO:0016020 / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Synechococcus sp. PCC 7335 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å | ||||||||||||
Authors | Gisriel, C.J. / Bryant, D.A. / Brudvig, G.W. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J Biol Chem / Year: 2022 Title: Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f. Authors: Christopher J Gisriel / Gaozhong Shen / Ming-Yang Ho / Vasily Kurashov / David A Flesher / Jimin Wang / William H Armstrong / John H Golbeck / Marilyn R Gunner / David J Vinyard / Richard J ...Authors: Christopher J Gisriel / Gaozhong Shen / Ming-Yang Ho / Vasily Kurashov / David A Flesher / Jimin Wang / William H Armstrong / John H Golbeck / Marilyn R Gunner / David J Vinyard / Richard J Debus / Gary W Brudvig / Donald A Bryant / Abstract: Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include ...Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700-800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the "red limit" for light required to drive photochemical catalysis of water oxidation. Changes to the architecture of FRL-PSII were previously unknown, and the positions of Chl d and Chl f molecules had only been proposed from indirect evidence. Here, we describe the 2.25 Å resolution cryo-EM structure of a monomeric FRL-PSII core complex from Synechococcus sp. PCC 7335 cells that were acclimated to FRL. We identify one Chl d molecule in the Chl position of the electron transfer chain and four Chl f molecules in the core antenna. We also make observations that enhance our understanding of PSII biogenesis, especially on the acceptor side of the complex where a bicarbonate molecule is replaced by a glutamate side chain in the absence of the assembly factor Psb28. In conclusion, these results provide a structural basis for the lower energy limit required to drive water oxidation, which is the gateway for most solar energy utilization on earth. | ||||||||||||
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 | 7sa3.cif.gz | 378.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sa3.ent.gz | 306.3 KB | Display | PDB format |
PDBx/mmJSON format | 7sa3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sa3_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 7sa3_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 7sa3_validation.xml.gz | 95.9 KB | Display | |
Data in CIF | 7sa3_validation.cif.gz | 126.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/7sa3 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/7sa3 | HTTPS FTP |
-Related structure data
Related structure data | 24943MC 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 II ... , 5 types, 5 molecules BCDIK
#2: Protein | Mass: 56440.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI1 |
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#3: Protein | Mass: 52375.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI2 |
#4: Protein | Mass: 39596.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI3, photosystem II |
#7: Protein/peptide | Mass: 4229.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WM03 |
#8: Protein/peptide | Mass: 5069.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WR12 |
-Cytochrome b559 subunit ... , 2 types, 2 molecules EF
#5: Protein | Mass: 9136.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WII1 |
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#6: Protein/peptide | Mass: 5023.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKJ2 |
-Protein / Protein/peptide , 2 types, 2 molecules AN
#1: Protein | Mass: 40111.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKH9 |
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#9: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) |
-Sugars , 2 types, 8 molecules
#16: Sugar | ChemComp-LMT / #18: Sugar | |
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-Non-polymers , 13 types, 278 molecules
#10: Chemical | ChemComp-CA / | ||||||||||||||||||||
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#11: Chemical | ChemComp-CL / | ||||||||||||||||||||
#12: Chemical | ChemComp-CLA / #13: Chemical | ChemComp-CL7 / | #14: Chemical | #15: Chemical | ChemComp-BCR / #17: Chemical | ChemComp-F6C / Mass: 905.457 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C55H68MgN4O6 / Feature type: SUBJECT OF INVESTIGATION #19: Chemical | #20: Chemical | ChemComp-FE2 / | #21: Chemical | ChemComp-PL9 / | #22: Chemical | ChemComp-LHG / | #23: Chemical | ChemComp-HEM / | #24: Water | ChemComp-HOH / | |
-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: Monomeric photosystem II from cyanobacteria acclimated to far-red light Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
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Source (natural) | Organism: Synechococcus sp. PCC 7335 (bacteria) |
Buffer solution | pH: 6.5 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 FIELD |
Image recording | Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315307 / Symmetry type: POINT |