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Yorodumi- PDB-6yp7: PSII-LHCII C2S2 supercomplex from Pisum sativum grown in high lig... -
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-Basic information
Entry | Database: PDB / ID: 6yp7 | ||||||
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Title | PSII-LHCII C2S2 supercomplex from Pisum sativum grown in high light conditions | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Cryo-EM / photosystem II / High Light | ||||||
Function / homology | Function and homology information plastoglobule / photosystem II oxygen evolving complex / photosystem II assembly / photosynthesis, light harvesting in photosystem I / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor ...plastoglobule / photosystem II oxygen evolving complex / photosystem II assembly / photosynthesis, light harvesting in photosystem I / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / response to light stimulus / photosynthetic electron transport in photosystem II / photosynthesis / protein stabilization / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pisum sativum (garden pea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Grinzato, A. / Albanese, P. / Zanotti, G. / Pagliano, C. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2020 Title: High-Light versus Low-Light: Effects on Paired Photosystem II Supercomplex Structural Rearrangement in Pea Plants. Authors: Alessandro Grinzato / Pascal Albanese / Roberto Marotta / Paolo Swuec / Guido Saracco / Martino Bolognesi / Giuseppe Zanotti / Cristina Pagliano / Abstract: In plant thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is ...In plant thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is dynamically adjusted in response to light cues, with the CS more abundant in high-light and the CSM in low-light. Paired PSII-LHCII supercomplexes interacting at their stromal surface from adjacent thylakoid membranes were previously suggested to mediate stacking. Here, we present the cryo-electron microscopy maps of paired CS and CSM supercomplexes isolated from pea plants grown in high-light and low-light, respectively. These maps show a different rotational offset between the two supercomplexes in the pair, responsible for modifying their reciprocal interaction and energetic connectivity. This evidence reveals a different way by which paired PSII-LHCII supercomplexes can mediate stacking at diverse irradiances. Electrostatic stromal interactions between LHCII trimers almost completely overlapping in the paired CS can be the main determinant by which PSII-LHCII supercomplexes mediate stacking in plants grown in high-light, whereas the mutual interaction of stromal N-terminal loops of two facing Lhcb4 subunits in the paired CSM can fulfil this task in plants grown in low-light. The high-light induced accumulation of the Lhcb4.3 protein in PSII-LHCII supercomplexes has been previously reported. Our cryo-electron microscopy map at 3.8 Å resolution of the CS supercomplex isolated from plants grown in high-light suggests the presence of the Lhcb4.3 protein revealing peculiar structural features of this high-light-specific antenna important for photoprotection. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6yp7.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6yp7.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6yp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yp7_validation.pdf.gz | 13.7 MB | Display | wwPDB validaton report |
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Full document | 6yp7_full_validation.pdf.gz | 14.4 MB | Display | |
Data in XML | 6yp7_validation.xml.gz | 353.7 KB | Display | |
Data in CIF | 6yp7_validation.cif.gz | 412.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6yp7 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6yp7 | HTTPS FTP |
-Related structure data
Related structure data | 10865MC 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
-Protein , 2 types, 8 molecules gnyGNYoO
#1: Protein | Mass: 23573.473 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: CAB8, LHCB1 / Production host: Pisum sativum (garden pea) / References: UniProt: P27490 #14: Protein | Mass: 26554.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: PSBO / Production host: Pisum sativum (garden pea) / References: UniProt: P14226 |
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-Photosystem II ... , 13 types, 26 molecules aAbBcCdDhHiIjJkKlLmMtTwWzZ
#2: Protein | Mass: 36972.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbA, pgiI / Production host: Pisum sativum (garden pea) / References: UniProt: P06585, photosystem II #3: Protein | Mass: 55659.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbB / Production host: Pisum sativum (garden pea) / References: UniProt: Q9XQR6 #4: Protein | Mass: 49275.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbC / Production host: Pisum sativum (garden pea) / References: UniProt: P06004 #5: Protein | Mass: 38220.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbD / Production host: Pisum sativum (garden pea) / References: UniProt: P06006, photosystem II #8: Protein | Mass: 6455.607 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbH / Production host: Pisum sativum (garden pea) / References: UniProt: Q9XQR3 #9: Protein/peptide | Mass: 3926.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbI / Production host: Pisum sativum (garden pea) / References: UniProt: D5MAJ9 #10: Protein/peptide | Mass: 3598.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbJ / Production host: Pisum sativum (garden pea) / References: UniProt: P13555 #11: Protein/peptide | Mass: 4287.155 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbK / Production host: Pisum sativum (garden pea) / References: UniProt: D5MAJ8 #12: Protein/peptide | Mass: 4366.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbL / Production host: Pisum sativum (garden pea) / References: UniProt: P60147 #13: Protein/peptide | Mass: 3641.425 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbM / Production host: Pisum sativum (garden pea) / References: UniProt: P69529 #15: Protein/peptide | Mass: 3692.472 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbT / Production host: Pisum sativum (garden pea) / References: UniProt: Q8HS25 #16: Protein | Mass: 5914.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ2 #18: Protein | Mass: 6555.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbZ, ycf9 / Production host: Pisum sativum (garden pea) / References: UniProt: Q32902 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules eEfF
#6: Protein | Mass: 8624.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbE / Production host: Pisum sativum (garden pea) / References: UniProt: P13554 #7: Protein/peptide | Mass: 3396.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbF / Production host: Pisum sativum (garden pea) / References: UniProt: P62096 |
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-Light harvesting chlorophyll a/b-binding protein ... , 2 types, 4 molecules rRsS
#19: Protein | Mass: 24460.893 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) #20: Protein | Mass: 23839.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ1*PLUS |
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-Protein/peptide / Sugars , 2 types, 12 molecules xX
#17: Protein/peptide | Mass: 3929.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: Q8VYY1 #35: Sugar | ChemComp-DGD / |
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-Non-polymers , 16 types, 315 molecules
#21: Chemical | ChemComp-CHL / #22: Chemical | ChemComp-CLA / #23: Chemical | ChemComp-LUT / ( #24: Chemical | ChemComp-XAT / ( #25: Chemical | ChemComp-NEX / ( #26: Chemical | ChemComp-LHG / #27: Chemical | #28: Chemical | #29: Chemical | ChemComp-CL / #30: Chemical | ChemComp-PHO / #31: Chemical | ChemComp-BCR / #32: Chemical | ChemComp-PL9 / #33: Chemical | ChemComp-SQD / #34: Chemical | #36: Chemical | ChemComp-LMG / #37: Chemical | |
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-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 |
-Sample preparation
Component | Name: PSII-LHCII C2S2 supercomplex / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL |
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Source (natural) | Organism: Pisum sativum (garden pea) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 |
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-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27942 / Symmetry type: POINT | ||||||||||||||||||||||||
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