[English] 日本語
![](img/lk-miru.gif)
- PDB-8jx3: alpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8jx3 | ||||||
---|---|---|---|---|---|---|---|
Title | alpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head 14-mer | ||||||
![]() |
| ||||||
![]() | TOXIN / pore / chimera protein / spy-catcher / spy-tag / dimer | ||||||
Function / homology | ![]() cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||
![]() | Ishii, Y. / Naito, K. / Yokoyama, T. / Tanaka, Y. / Matsuura, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer Authors: Ishii, Y. / Naito, K. / Yokoyama, T. / Tanaka, Y. / Matsuura, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 716.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 595.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 36689MC ![]() 8jx2C 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
#1: Protein | Mass: 46977.469 Da / Num. of mol.: 7 / Mutation: G122S,K147R,K237C Source method: isolated from a genetically manipulated source Details: 300-412:SpyCatcher / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 36777.898 Da / Num. of mol.: 7 / Mutation: G122S,K147R,K237C Source method: isolated from a genetically manipulated source Details: 300-315:SpyTag / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher and spy-tag Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||
Buffer solution | pH: 7.6 / Details: 20mM HEPES-KOH[pH7.6], 50mM Potassium glutamate | ||||||||||||
Buffer component |
| ||||||||||||
Specimen | Conc.: 0.58 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
---|---|
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 349752 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|