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Open data
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Basic information
Entry | Database: PDB / ID: 4lhy | ||||||
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Title | Crystal structure of GDP-bound Rab8:Rabin8 | ||||||
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![]() | PROTEIN TRANSPORT / Small GTPase / Guanine Nucleotide Exchange Factor | ||||||
Function / homology | ![]() Golgi to plasma membrane transport vesicle / protein localization to motile cilium / ciliary basal body-plasma membrane docking / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / protein localization to organelle / negative regulation of filopodium assembly / proximal dendrite ...Golgi to plasma membrane transport vesicle / protein localization to motile cilium / ciliary basal body-plasma membrane docking / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / protein localization to organelle / negative regulation of filopodium assembly / proximal dendrite / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / BBSome-mediated cargo-targeting to cilium / RAB geranylgeranylation / Golgi to plasma membrane transport / myosin V binding / positive regulation of cilium assembly / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / protein localization to cilium / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / protein targeting to membrane / ciliary membrane / ciliary base / Golgi organization / exocytosis / protein secretion / cilium assembly / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / centriole / protein tyrosine kinase binding / axonogenesis / small monomeric GTPase / ciliary basal body / guanyl-nucleotide exchange factor activity / 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 / cilium / small GTPase binding / autophagy / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / protein transport / synaptic vesicle / lamellipodium / GTPase binding / midbody / dendritic spine / postsynaptic density / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
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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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.3 KB | Display | ![]() |
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PDB format | ![]() | 206.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4lhvC ![]() 4lhwC ![]() 4lhxC ![]() 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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Components
#1: Protein | Mass: 21259.371 Da / Num. of mol.: 2 / Fragment: unp residues 1-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 8982.210 Da / Num. of mol.: 4 / Fragment: unp residues 173-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-SO4 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution ...Details: Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hour at 4 C, 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: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20.1 Å / Num. all: 20523 / Num. obs: 20118 / % possible obs: 98 % / Observed criterion σ(F): 8.3 / Observed criterion σ(I): 13.56 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YZQ Resolution: 3.1→20.08 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.852 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.459 / ESU R Free: 0.494 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.471 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→20.08 Å
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Refine LS restraints |
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