+Open data
-Basic information
Entry | Database: PDB / ID: 2qyw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse vti1b Habc domain | ||||||
Components | Vesicle transport through interaction with t-SNAREs 1B homolog | ||||||
Keywords | PROTEIN TRANSPORT / ENDOCYTOSIS / Habc domain | ||||||
Function / homology | Function and homology information vesicle fusion with Golgi apparatus / Golgi to vacuole transport / Platelet degranulation / chloride channel inhibitor activity / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / retrograde transport, endosome to Golgi / regulation of protein localization to plasma membrane / vesicle-mediated transport ...vesicle fusion with Golgi apparatus / Golgi to vacuole transport / Platelet degranulation / chloride channel inhibitor activity / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / retrograde transport, endosome to Golgi / regulation of protein localization to plasma membrane / vesicle-mediated transport / SNARE binding / macroautophagy / intracellular protein transport / ER to Golgi transport vesicle membrane / recycling endosome / recycling endosome membrane / synaptic vesicle / late endosome membrane / early endosome membrane / vesicle / membrane => GO:0016020 / lysosomal membrane / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å | ||||||
Authors | Miller, S.E. / Collins, B.M. / McCoy, A.J. / Robinson, M.S. / Owen, D.J. | ||||||
Citation | Journal: Nature / Year: 2007 Title: A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles. Authors: Miller, S.E. / Collins, B.M. / McCoy, A.J. / Robinson, M.S. / Owen, D.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qyw.cif.gz | 29.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qyw.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/2qyw ftp://data.pdbj.org/pub/pdb/validation_reports/qy/2qyw | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11974.978 Da / Num. of mol.: 1 / Fragment: Habc Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vti1b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/plysS / References: UniProt: Q91XH6, UniProt: O88384*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.22 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM Tris, 30% ethanol and 20% glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→79 Å / Num. obs: 6751 / % possible obs: 96.9 % / Observed criterion σ(F): 4 / Redundancy: 9.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4 / % possible all: 96.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.884 / SU B: 9.984 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.105 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|