[English] 日本語
![](img/lk-miru.gif)
- PDB-2a9u: Structure of the N-terminal domain of Human Ubiquitin carboxyl-te... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2a9u | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8) | ||||||
![]() | Ubiquitin carboxyl-terminal hydrolase 8 | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of lysosomal protein catabolic process / protein K48-linked deubiquitination / endosome organization / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, E. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, E. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8). Authors: Avvakumov, G.V. / Walker, J.R. / Xue, S. / Finerty Jr., P.J. / Mackenzie, F. / Newman, E.M. / Dhe-Paganon, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is a homodimer. |
-
Components
#1: Protein | Mass: 17026.145 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 53.77 % |
---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 27% PEG3350, 0.2 M Li2SO4, 0.1 M bisTris, pH 5.6, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Jul 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→33.81 Å / Num. all: 18987 / Num. obs: 18987 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.15 / Num. unique all: 16 / % possible all: 80.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.08 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→33.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.151 Å / Total num. of bins used: 20
|