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Yorodumi- PDB-1ujj: VHS domain of human GGA1 complexed with C-terminal peptide from BACE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ujj | ||||||
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Title | VHS domain of human GGA1 complexed with C-terminal peptide from BACE | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/Hydrolase / PROTEIN-PEPTIDE COMPLEX / PROTEIN TRANSPORT / ADAPTOR PROTEIN / PROTEIN TRANSPORT-Hydrolase COMPLEX | ||||||
Function / homology | Function and homology information protein localization to ciliary membrane / Golgi to plasma membrane protein transport / Golgi to plasma membrane transport / protein localization to cell surface / retrograde transport, endosome to Golgi / 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 protein transport / Golgi to plasma membrane transport / protein localization to cell surface / retrograde transport, endosome to Golgi / 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 / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / cellular response to copper ion / hippocampal mossy fiber to CA3 synapse / presynaptic modulation of chemical synaptic transmission / multivesicular body / phosphatidylinositol binding / ubiquitin binding / response to lead ion / intracellular protein transport / protein catabolic process / trans-Golgi network / protein localization / protein processing / recycling endosome / small GTPase binding / cellular response to amyloid-beta / positive regulation of protein catabolic process / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / amyloid-beta binding / peptidase activity / early endosome membrane / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / axon / endoplasmic reticulum lumen / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Shiba, T. / Kametaka, S. / Kawasaki, M. / Shibata, M. / Waguri, S. / Uchiyama, Y. / Wakatsuki, S. | ||||||
Citation | Journal: TRAFFIC / Year: 2004 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ujj.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ujj.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ujj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/1ujj ftp://data.pdbj.org/pub/pdb/validation_reports/uj/1ujj | HTTPS FTP |
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-Related structure data
Related structure data | 1ujkC 1jwgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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.) Homo sapiens (human) / Plasmid: pGEX4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UJY5 #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 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 54.69 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JWG Resolution: 2.6→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→40 Å
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Refine LS restraints |
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