[English] 日本語

- PDB-9jow: Cryo-EM structure of the myxol-bound light-driven chloride ion-pu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 9jow | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the myxol-bound light-driven chloride ion-pumping rhodopsin, NM-R3 | |||||||||||||||||||||||||||
![]() | Chloride pumping rhodopsin | |||||||||||||||||||||||||||
![]() | MEMBRANE PROTEIN / chloride ion-pumping rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin | |||||||||||||||||||||||||||
Function / homology | ![]() | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å | |||||||||||||||||||||||||||
![]() | Hosaka, T. / Shirouzu, M. | |||||||||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||||||||
![]() | ![]() Title: Intracellular carotenoids enhance the pump activation of microbial rhodopsin in two ways: The light-harvesting antenna and the photocycle acceleration Authors: Fujiwara, T. / Hosaka, T. / Hasegawa-Takano, M. / Nishimura, Y. / Tominaga, K. / Mori, K. / Nishino, S. / Kawasaki, Y. / Takahashi, Y. / Uchikubo-Kamo, T. / Hanada, K. / Takaichi, S. / ...Authors: Fujiwara, T. / Hosaka, T. / Hasegawa-Takano, M. / Nishimura, Y. / Tominaga, K. / Mori, K. / Nishino, S. / Kawasaki, Y. / Takahashi, Y. / Uchikubo-Kamo, T. / Hanada, K. / Takaichi, S. / Inoue, K. / Shirouzu, M. / Yoshizawa, S. | |||||||||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 303.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 67.8 KB | Display | |
Data in CIF | ![]() | 90.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 61687MC ![]() 9jouC ![]() 9jovC ![]() 9joxC 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
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 30710.936 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 11 types, 241 molecules 


















#2: Chemical | ChemComp-RET / #3: Chemical | ChemComp-A1L4O / ( Mass: 584.871 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O3 #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PC1 / #6: Chemical | ChemComp-PLC / #7: Chemical | ChemComp-R16 / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-C14 / #11: Chemical | ChemComp-D10 / | #12: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: NM-R3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
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: 800 nm |
Image recording | Electron dose: 60.425 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 791219 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.48→2.48 Å / Cor.coef. Fo:Fc: 0.833 / SU B: 4.051 / SU ML: 0.08 / ESU R: 0.205 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.513 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 11677 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|