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Open data
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Basic information
Entry | Database: PDB / ID: 1yu9 | ||||||
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Title | GppNHp-Bound Rab4A | ||||||
![]() | GTP-binding protein | ||||||
![]() | PROTEIN TRANSPORT / Rab GTPase / Rab4 / vesicular trafficking | ||||||
Function / homology | ![]() postsynaptic recycling endosome / Rab protein signal transduction / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / antigen processing and presentation / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / vesicle-mediated transport ...postsynaptic recycling endosome / Rab protein signal transduction / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / antigen processing and presentation / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / vesicle-mediated transport / small monomeric GTPase / G protein activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / recycling endosome membrane / GDP binding / protein transport / early endosome membrane / vesicle / GTPase activity / GTP binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.1 KB | Display | ![]() |
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PDB format | ![]() | 38.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769.3 KB | Display | ![]() |
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Full document | ![]() | 770 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yvdC ![]() 1yzkC ![]() 1yzlC ![]() 1yzmC ![]() 1yznC ![]() 1yzqC ![]() 1yztC ![]() 1yzuC ![]() 1z06C ![]() 1z07C ![]() 1z08C ![]() 1z0aC ![]() 1z0dC ![]() 1z0fC ![]() 1z0iC ![]() 1z0jC ![]() 1z0kC ![]() 1z22C ![]() 1z2aC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19674.312 Da / Num. of mol.: 1 / Fragment: GTPase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-GNP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Ammonium sulfate, MES, Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 23, 2002 |
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: 2.05→50 Å / Num. obs: 13803 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.078 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 2011 / Rsym value: 0.282 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Rab3a polyalanine Resolution: 2.07→7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 16.527 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.067→2.116 Å
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