+Open data
-Basic information
Entry | Database: PDB / ID: 1yzk | ||||||
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Title | GppNHp bound Rab11 GTPase | ||||||
Components | Ras-related protein Rab-11A | ||||||
Keywords | PROTEIN TRANSPORT / Rab GTPase / Rab11 / Vesicular trafficking | ||||||
Function / homology | Function and homology information regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / regulation of cilium assembly / exosomal secretion ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / melanosome transport / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / protein localization to cilium / multivesicular body assembly / dynein light intermediate chain binding / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / phagocytic vesicle / transport vesicle / vesicle-mediated transport / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / small monomeric GTPase / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / neuron projection development / endocytic vesicle membrane / cytoplasmic vesicle / microtubule binding / vesicle / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / Golgi apparatus / protein-containing complex / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yzk.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yzk.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzk ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzk | HTTPS FTP |
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-Related structure data
Related structure data | 1yu9C 1yvdC 1yzlC 1yzmC 1yznC 1yzqC 1yztC 1yzuC 1z06C 1z07C 1z08C 1z0aC 1z0dC 1z0fC 1z0iC 1z0jC 1z0kC 1z22C 1z2aC 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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Unit cell |
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-Components
#1: Protein | Mass: 20752.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: P62491 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: NaCl, Glycerol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2003 |
Radiation | Monochromator: confocal blue optic device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 14293 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.058 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 7 % / Mean I/σ(I) obs: 7.6 / Num. unique all: 1139 / Rsym value: 0.252 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Polyalanine Rab5c Resolution: 2→6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.692 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.174 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.315 Å2
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.046 Å / Total num. of bins used: 20
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