+Open data
-Basic information
Entry | Database: PDB / ID: 1o3y | |||||||||
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Title | Crystal structure of mouse ARF1 (delta17-Q71L), GTP form | |||||||||
Components | ADP-ribosylation factor 1ARF1 | |||||||||
Keywords | PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Golgi to transport vesicle transport / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic / mitotic cleavage furrow ingression ...synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Golgi to transport vesicle transport / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic / mitotic cleavage furrow ingression / positive regulation of ER to Golgi vesicle-mediated transport / Lysosome Vesicle Biogenesis / COPI-mediated anterograde transport / regulation of receptor internalization / very-low-density lipoprotein particle assembly / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the plasma membrane / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of calcium ion-dependent exocytosis / postsynaptic actin cytoskeleton organization / Golgi Associated Vesicle Biogenesis / MHC class II antigen presentation / dendritic spine organization / long-term synaptic depression / positive regulation of sodium ion transmembrane transport / positive regulation of dendritic spine development / cell leading edge / positive regulation of endocytosis / intracellular copper ion homeostasis / endomembrane system / vesicle-mediated transport / sarcomere / small monomeric GTPase / actin filament organization / positive regulation of protein secretion / intracellular protein transport / cellular response to virus / GDP binding / late endosome / protein transport / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / magnesium ion binding / protein-containing complex / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Shiba, T. / Kawasaki, M. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport Authors: Shiba, T. / Kawasaki, M. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o3y.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o3y.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 1o3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/1o3y ftp://data.pdbj.org/pub/pdb/validation_reports/o3/1o3y | HTTPS FTP |
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-Related structure data
Related structure data | 1j2jC 1o3xC 1hfv 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18951.615 Da / Num. of mol.: 2 / Fragment: RESIDUES 18-181 / Mutation: Q71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pProEX HT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P84078 #2: Chemical | #3: Chemical | #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: 1.82 Å3/Da / Density % sol: 31.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG3350, ammonium acetate, acetate, pH 4.0, 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: BL-6A / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2002 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 44086 / Num. obs: 44072 / % possible obs: 89.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.1 / % possible all: 62.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HFV 1hfv Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.546 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.332 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /
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