[English] 日本語
![](img/lk-miru.gif)
- PDB-6yp7: PSII-LHCII C2S2 supercomplex from Pisum sativum grown in high lig... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6yp7 | ||||||
---|---|---|---|---|---|---|---|
Title | PSII-LHCII C2S2 supercomplex from Pisum sativum grown in high light conditions | ||||||
![]() |
| ||||||
![]() | PHOTOSYNTHESIS / Cryo-EM / photosystem II / High Light | ||||||
Function / homology | ![]() plastoglobule / photosystem II assembly / photosystem II oxygen evolving complex / 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 assembly / photosystem II oxygen evolving complex / 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 / 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: 3.8 Å | ||||||
![]() | Grinzato, A. / Albanese, P. / Zanotti, G. / Pagliano, C. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 13.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 14.4 MB | Display | |
Data in XML | ![]() | 353.7 KB | Display | |
Data in CIF | ![]() | 412.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10865MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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.) ![]() ![]() ![]() ![]() #14: Protein | Mass: 26554.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-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.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 55659.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 49275.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Protein | Mass: 38220.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #8: Protein | Mass: 6455.607 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #9: Protein/peptide | Mass: 3926.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #10: Protein/peptide | Mass: 3598.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #11: Protein/peptide | Mass: 4287.155 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #12: Protein/peptide | Mass: 4366.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #13: Protein/peptide | Mass: 3641.425 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #15: Protein/peptide | Mass: 3692.472 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #16: Protein | Mass: 5914.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #18: Protein | Mass: 6555.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-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.) ![]() ![]() ![]() ![]() #7: Protein/peptide | Mass: 3396.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-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.) ![]() ![]() ![]() ![]() #20: Protein | Mass: 23839.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Protein/peptide / Sugars , 2 types, 12 molecules xX![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#17: Protein/peptide | Mass: 3929.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #35: Sugar | ChemComp-DGD / |
---|
-Non-polymers , 16 types, 315 molecules ![](data/chem/img/CHL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/NEX.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/NEX.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HEM.gif)
#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 | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Microscopy | Model: FEI TITAN KRIOS | ||||||||||||
Electron gun | Electron source: ![]() | ||||||||||||
Electron lens | Mode: BRIGHT FIELD | ||||||||||||
Image recording |
|
-
Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | ||||||||||||||||||||||||
Refine LS restraints |
|