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Yorodumi- PDB-3g2v: VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g2v | ||||||
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Title | VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / ADP-ribosylation factor binding protein GGA1 / VHS / acidic-cluster dileucine signal / Sortilin | ||||||
Function / homology | Function and homology information neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / myotube differentiation / protein localization to ciliary membrane / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / retromer complex binding / maintenance of synapse structure / Golgi to endosome transport / nerve growth factor receptor activity ...neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / myotube differentiation / protein localization to ciliary membrane / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / retromer complex binding / maintenance of synapse structure / Golgi to endosome transport / nerve growth factor receptor activity / Golgi to lysosome transport / vesicle organization / endosome transport via multivesicular body sorting pathway / Golgi to plasma membrane protein transport / nerve growth factor binding / protein targeting to lysosome / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / protein localization to cell surface / retrograde transport, endosome to Golgi / TBC/RABGAPs / clathrin-coated vesicle / negative regulation of fat cell differentiation / Golgi cisterna membrane / Golgi Associated Vesicle Biogenesis / endosome to lysosome transport / glucose import / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / neuropeptide signaling pathway / clathrin-coated pit / phosphatidylinositol binding / ossification / ubiquitin binding / intracellular protein transport / protein catabolic process / response to insulin / trans-Golgi network / protein localization / small GTPase binding / endocytosis / positive regulation of protein catabolic process / cytoplasmic vesicle / early endosome membrane / regulation of gene expression / nuclear membrane / lysosome / early endosome / endosome membrane / G protein-coupled receptor signaling pathway / Amyloid fiber formation / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / protein-containing complex / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cramer, J.F. / Behrens, M.A. / Gustafsen, C. / Oliveira, C.L.P. / Pedersen, J.S. / Madsen, P. / Petersen, C.M. / Thirup, S.S. | ||||||
Citation | Journal: Traffic / Year: 2010 Title: GGA autoinhibition revisited Authors: Cramer, J.F. / Gustafsen, C. / Behrens, M.A. / Oliveira, C.L.P. / Pedersen, J.S. / Madsen, P. / Petersen, C.M. / Thirup, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g2v.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g2v.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 3g2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/3g2v ftp://data.pdbj.org/pub/pdb/validation_reports/g2/3g2v | HTTPS FTP |
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-Related structure data
Related structure data | 3g2sC 3g2tC 3g2uC 3g2wC 1jwfS C: citing same article (ref.) S: Starting model for refinement |
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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: 16958.564 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-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RIL / References: UniProt: Q9UJY5 #2: Protein/peptide | Mass: 1575.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: Q99523 #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.15 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 16%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 3, 2008 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.5 Å / Num. all: 21651 / Num. obs: 21642 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.92 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 8.13 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.44 / Num. unique all: 2767 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JWF Resolution: 2.1→43.47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.846 / SU B: 8.964 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2.01 / ESU R: 0.215 / ESU R Free: 0.192 / Phase error: 22.06 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.857 Å2 / ksol: 0.369 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.01 Å2 / Biso mean: 39.744 Å2 / Biso min: 16.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→43.47 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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