[English] 日本語
![](img/lk-miru.gif)
- PDB-8tow: Structure of a mutated photosystem II complex reveals perturbatio... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8tow | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a mutated photosystem II complex reveals perturbation of the oxygen-evolving complex | ||||||
![]() |
| ||||||
![]() | PHOTOSYNTHESIS / photosystem II / oxygen-evolving complex / D1-D170E / S1 state / transition metals / metalloenzyme | ||||||
Function / homology | ![]() plasma membrane-derived thylakoid photosystem II / photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / 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 ...plasma membrane-derived thylakoid photosystem II / photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / 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 / 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 / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / calcium ion binding / heme binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å | ||||||
![]() | Flesher, D.A. / Liu, J. / Wang, J. / Gisriel, C.J. / Yang, K.R. / Batista, V.S. / Debus, R.J. / Brudvig, G.W. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels Authors: Flesher, D.A. / Brudvig, G.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 9.9 MB | Display | |
Data in XML | ![]() | 265.9 KB | Display | |
Data in CIF | ![]() | 349.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 41460MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoRrTtUuXx...
#1: Protein | Mass: 39758.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 55954.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 50344.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 39519.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 7120.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein/peptide | Mass: 4338.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein/peptide | Mass: 3976.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein/peptide | Mass: 5114.127 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein/peptide | Mass: 4476.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein/peptide | Mass: 3910.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 29939.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein/peptide | Mass: 4204.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein/peptide | Mass: 3571.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 14256.163 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein/peptide | Mass: 4189.036 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein/peptide | Mass: 4143.993 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein | Mass: 6736.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9454.577 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein/peptide | Mass: 4935.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Protein , 2 types, 4 molecules QqVv
#14: Protein | Mass: 16494.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 17901.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Sugars , 2 types, 72 molecules ![](data/chem/img/LMT.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#31: Sugar | ChemComp-LMT / #34: Sugar | ChemComp-DGD / |
---|
-Non-polymers , 15 types, 1430 molecules ![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#22: Chemical | #23: Chemical | #24: Chemical | ChemComp-CL / #25: Chemical | ChemComp-CLA / #26: Chemical | ChemComp-PHO / #27: Chemical | ChemComp-BCR / #28: Chemical | ChemComp-LMG / #29: Chemical | ChemComp-PL9 / #30: Chemical | ChemComp-SQD / #32: Chemical | #33: Chemical | ChemComp-LHG / #35: Chemical | ChemComp-HEM / #36: Chemical | #37: Chemical | ChemComp-CA / #38: 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: photosystem II / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6.8 |
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 38 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129229 / Symmetry type: POINT |