+Open data
-Basic information
Entry | Database: PDB / ID: 2fu5 | ||||||
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Title | structure of Rab8 in complex with MSS4 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / MSS4:Rab8 protein complex / GEF:GTPase nucleotide free complex / nucleotide exchange via unfolding of nucleotide binding region | ||||||
Function / homology | Function and homology information VxPx cargo-targeting to cilium / TBC/RABGAPs / neurotransmitter receptor transport to postsynaptic membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / small GTPase binding => GO:0031267 / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / post-Golgi vesicle-mediated transport ...VxPx cargo-targeting to cilium / TBC/RABGAPs / neurotransmitter receptor transport to postsynaptic membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / small GTPase binding => GO:0031267 / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / post-Golgi vesicle-mediated transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / Anchoring of the basal body to the plasma membrane / Regulation of PLK1 Activity at G2/M Transition / regulation of exocytosis / myosin V binding / trans-Golgi network transport vesicle / non-motile cilium / vesicle docking involved in exocytosis / ciliary base / small GTPase-mediated signal transduction / protein secretion / cilium assembly / phagocytic vesicle / centriole / axonogenesis / ciliary basal body / guanyl-nucleotide exchange factor activity / regulation of autophagy / protein localization to plasma membrane / regulation of long-term neuronal synaptic plasticity / cytoplasmic vesicle membrane / recycling endosome / cilium / autophagy / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / regulation of protein localization / protein transport / synaptic vesicle / midbody / cytoplasmic vesicle / dendritic spine / membrane fusion / postsynaptic density / endosome / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / synapse / dendrite / GTP binding / protein kinase binding / Golgi apparatus / zinc ion binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Itzen, A. / Pylypenko, O. / Goody, R.S. / Rak, A. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Nucleotide exchange via local protein unfolding-structure of Rab8 in complex with MSS4 Authors: Itzen, A. / Pylypenko, O. / Goody, R.S. / Alexandrov, K. / Rak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fu5.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fu5.ent.gz | 95.1 KB | Display | PDB format |
PDBx/mmJSON format | 2fu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/2fu5 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/2fu5 | HTTPS FTP |
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-Related structure data
Related structure data | 1hxrS 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: 13198.093 Da / Num. of mol.: 2 / Fragment: residues 11-123 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RABIF, MSS4, RASGRF3 / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P47224 #2: Protein | Mass: 20953.076 Da / Num. of mol.: 2 / Fragment: residues 1-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab8a, Mel, Rab8 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P55258 #3: Chemical | #4: Chemical | #5: 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: 2.41 Å3/Da / Density % sol: 48.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 20% PEG3350, 50mM TrisHCL pH 9.0, 0.2M magnesium acetate, 0.15% (w/v) 1,2,3-heptanetriole, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.17 Å / Num. all: 40718 / Num. obs: 40718 / % possible obs: 94.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2→2.05 Å / % possible all: 74.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1hxr Resolution: 2→19.17 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / SU B: 3.901 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.175 / Stereochemistry target values: Engh & Huber
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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: 44.426 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20 /
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