+Open data
-Basic information
Entry | Database: PDB / ID: 3n1b | ||||||
---|---|---|---|---|---|---|---|
Title | C-terminal domain of Vps54 subunit of the GARP complex | ||||||
Components | Vacuolar protein sorting-associated protein 54Vacuole | ||||||
Keywords | TRANSPORT PROTEIN / spinal muscular atrophy / vesicle trafficking / Golgi apparatus / tethering complex / GARP | ||||||
Function / homology | Function and homology information neural tissue regeneration / GARP complex / Retrograde transport at the Trans-Golgi-Network / skeletal muscle tissue growth / post-embryonic forelimb morphogenesis / musculoskeletal movement / vesicle-mediated cholesterol transport / thrombin-activated receptor signaling pathway / spermatid differentiation / L-glutamate import ...neural tissue regeneration / GARP complex / Retrograde transport at the Trans-Golgi-Network / skeletal muscle tissue growth / post-embryonic forelimb morphogenesis / musculoskeletal movement / vesicle-mediated cholesterol transport / thrombin-activated receptor signaling pathway / spermatid differentiation / L-glutamate import / sphingolipid catabolic process / ubiquitin recycling / Golgi to vacuole transport / neuromuscular synaptic transmission / apoptotic DNA fragmentation / limb morphogenesis / protein targeting to ER / cellular response to progesterone stimulus / neuroinflammatory response / protein targeting to vacuole / protein targeting to lysosome / vacuole organization / neurofilament cytoskeleton organization / microglia differentiation / negative regulation of motor neuron apoptotic process / astrocyte differentiation / synaptic transmission, GABAergic / protein localization to cell surface / retrograde transport, endosome to Golgi / regulation of growth / limb development / motor neuron apoptotic process / motor behavior / lysosomal transport / syntaxin binding / homeostasis of number of cells / striated muscle contraction / homeostasis of number of cells within a tissue / skeletal muscle tissue development / respiratory electron transport chain / mitochondrion organization / neuron projection morphogenesis / synaptic transmission, glutamatergic / trans-Golgi network / protein localization / intracellular calcium ion homeostasis / response to calcium ion / protein transport / gene expression / neuron apoptotic process / in utero embryonic development / response to antibiotic / synapse / perinuclear region of cytoplasm / Golgi apparatus / mitochondrion / nucleoplasm / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.398 Å | ||||||
Authors | Perez-Victoria, F.J. / Abascal-Palacios, G. / Tascon, I. / Kajava, A. / Pioro, E.P. / Bonifacino, J.S. / Hierro, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for the wobbler mouse neurodegenerative disorder caused by mutation in the Vps54 subunit of the GARP complex. Authors: Perez-Victoria, F.J. / Abascal-Palacios, G. / Tascon, I. / Kajava, A. / Magadan, J.G. / Pioro, E.P. / Bonifacino, J.S. / Hierro, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3n1b.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3n1b.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 3n1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/3n1b ftp://data.pdbj.org/pub/pdb/validation_reports/n1/3n1b | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16499.338 Da / Num. of mol.: 2 / Fragment: residues 836-974 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps54 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SPW0 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.94 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 23% PEG3350, 0.1M BisTris, 0.1M I3C, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.3 % / Av σ(I) over netI: 12.34 / Number: 57298 / Rmerge(I) obs: 0.07 / Χ2: 1.02 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 9115 / % possible obs: 99.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.398→50 Å / Num. obs: 11565 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Χ2: 1.035 / Net I/σ(I): 18.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing dm | FOM : 0.62 / FOM acentric: 0.63 / FOM centric: 0.59 / Reflection: 11554 / Reflection acentric: 10298 / Reflection centric: 1256 | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phasing dm shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.398→30.976 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.786 / SU ML: 0.33 / σ(F): 0 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.967 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.91 Å2 / Biso mean: 50.553 Å2 / Biso min: 24.29 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.398→30.976 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
|