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Open data
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Basic information
Entry | Database: PDB / ID: 4lhv | ||||||
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Title | Crystal structure of Rab8 in its inactive GDP-bound form | ||||||
![]() | Ras-related protein Rab-8A | ||||||
![]() | PROTEIN TRANSPORT / Small GTPase | ||||||
Function / homology | ![]() neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / regulation of exocytosis / trans-Golgi network transport vesicle ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / regulation of exocytosis / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / protein localization to cilium / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / protein secretion / cilium assembly / Anchoring of the basal body to the plasma membrane / centriole / phagocytic vesicle / axonogenesis / protein tyrosine kinase binding / small monomeric GTPase / ciliary basal body / trans-Golgi network membrane / regulation of autophagy / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / small GTPase binding / autophagy / cilium / recycling endosome membrane / cellular response to insulin stimulus / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / midbody / dendritic spine / postsynaptic density / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, Z. / Hou, X.M. / Goody, R.S. / Itzen, A. | ||||||
![]() | ![]() Title: Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB. Authors: Guo, Z. / Hou, X. / Goody, R.S. / Itzen, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345.6 KB | Display | ![]() |
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PDB format | ![]() | 284.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lhwC ![]() 4lhxC ![]() 4lhyC ![]() 4lhzC ![]() 4li0C ![]() 1yzqS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 19967.920 Da / Num. of mol.: 5 / Fragment: unp residues 6-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM ...Details: All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 67917 / Num. obs: 67378 / % possible obs: 99.2 % / Observed criterion σ(F): 3.8 / Observed criterion σ(I): 19.16 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YZQ Resolution: 1.95→19.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.064 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.69 / ESU R Free: 0.16 / 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: 36.651 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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