[English] 日本語
![](img/lk-miru.gif)
- PDB-1ujj: VHS domain of human GGA1 complexed with C-terminal peptide from BACE -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ujj | ||||||
---|---|---|---|---|---|---|---|
Title | VHS domain of human GGA1 complexed with C-terminal peptide from BACE | ||||||
![]() |
| ||||||
![]() | PROTEIN TRANSPORT/Hydrolase / PROTEIN-PEPTIDE COMPLEX / PROTEIN TRANSPORT / ADAPTOR PROTEIN / PROTEIN TRANSPORT-Hydrolase COMPLEX | ||||||
Function / homology | ![]() protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / phosphatidylinositol binding / ubiquitin binding / response to lead ion / intracellular protein transport / protein catabolic process / protein localization / trans-Golgi network / recycling endosome / protein processing / small GTPase binding / positive regulation of protein catabolic process / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / early endosome membrane / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / lysosome / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / protein-containing complex / proteolysis / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shiba, T. / Kametaka, S. / Kawasaki, M. / Shibata, M. / Waguri, S. / Uchiyama, Y. / Wakatsuki, S. | ||||||
![]() | ![]() Title: Insights into the Phosphoregulation of beta-Secretase Sorting Signal by the VHS Domain of GGA1 Authors: Shiba, T. / Kametaka, S. / Kawasaki, M. / Shibata, M. / Waguri, S. / Uchiyama, Y. / Wakatsuki, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 66.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 50.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.7 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ujkC ![]() 1jwgS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16814.436 Da / Num. of mol.: 2 / Fragment: VHS domain, N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 1390.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized peptide References: UniProt: P56817, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 54.69 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: PEG 5000MME, di-Ammonium hydrogen phosphate, Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2003 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 10872 / Num. obs: 10857 / % possible obs: 99.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 99.7 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JWG Resolution: 2.6→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→40 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|