[English] 日本語
![](img/lk-miru.gif)
- PDB-6wj6: Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PC... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6wj6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803 | |||||||||
![]() |
| |||||||||
![]() | PHOTOSYNTHESIS / Photosystem / oxidoreductase / water-splitting / photoactivation | |||||||||
Function / homology | ![]() plasma membrane-derived thylakoid photosystem II / oxygen evolving activity / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding ...plasma membrane-derived thylakoid photosystem II / oxygen evolving activity / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / 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 / electron transfer activity / protein stabilization / iron ion binding / heme binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å | |||||||||
![]() | Gisriel, C.J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex Authors: Gisriel, C.J. / Zhou, K. / Huang, H. / Debus, R.J. / Xiong, Y. / Brudvig, G.W. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 448.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 367.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 110.5 KB | Display | |
Data in CIF | ![]() | 141.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 21690MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Photosystem II ... , 11 types, 11 molecules ABCDHIKLMTX
#1: Protein | Mass: 39744.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P16033, photosystem II |
---|---|
#2: Protein | Mass: 55954.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P05429 |
#3: Protein | Mass: 50330.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P09193 |
#4: Protein | Mass: 39519.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P09192, photosystem II |
#7: Protein | Mass: 7120.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P14835 |
#8: Protein/peptide | Mass: 4310.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: Q54697 |
#9: Protein/peptide | Mass: 5114.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P15819 |
#10: Protein/peptide | Mass: 4476.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: Q55354 |
#11: Protein/peptide | Mass: 3882.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P72701 |
#12: Protein/peptide | Mass: 3543.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P74787 |
#13: Protein/peptide | Mass: 4189.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P72575 |
-Cytochrome b559 subunit ... , 2 types, 2 molecules EF
#5: Protein | Mass: 9454.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P09190 |
---|---|
#6: Protein/peptide | Mass: 4935.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: PCC 6803 / Kazusa / References: UniProt: P09191 |
-Sugars , 2 types, 4 molecules ![](data/chem/img/LMT.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#21: Sugar | #22: Sugar | |
---|
-Non-polymers , 13 types, 267 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FME.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FME.gif)
![](data/chem/img/HOH.gif)
#14: Chemical | ChemComp-FE2 / | ||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#15: Chemical | ChemComp-CLA / #16: Chemical | #17: Chemical | ChemComp-BCR / #18: Chemical | ChemComp-SQD / #19: Chemical | #20: Chemical | #23: Chemical | ChemComp-CL / | #24: Chemical | ChemComp-BCT / | #25: Chemical | ChemComp-LHG / #26: Chemical | ChemComp-HEM / | #27: Chemical | #28: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: apo-Photosystem II / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL |
---|---|
Molecular weight | Value: 0.267067 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() Strain: PCC 6803 / Kazusa |
Buffer solution | pH: 7 Details: 10 mM HEPES pH 7.0 100 mM NaCl 0.03% beta-dodecylmaltoside |
Specimen | Conc.: 0.025 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse single particles |
Specimen support | 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: 298 K |
-
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 | Electron dose: 48.07 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
EM software | Name: RELION / Version: 3.1 / Category: 3D reconstruction |
---|---|
CTF correction | Type: NONE |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212640 / Symmetry type: POINT |