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Yorodumi- PDB-1oix: X-ray structure of the small G protein Rab11a in complex with GDP... -
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-Basic information
Entry | Database: PDB / ID: 1oix | ||||||
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Title | X-ray structure of the small G protein Rab11a in complex with GDP and Pi | ||||||
Components | RAS-RELATED PROTEIN RAB-11A | ||||||
Keywords | PROTEIN TRANSPORT / SMALL G PROTEIN / INTRACELLULAR TRAFFICKING / GTP-BINDING / LIPOPROTEIN / PRENYLATION | ||||||
Function / homology | Function and homology information Anchoring of the basal body to the plasma membrane / VxPx cargo-targeting to cilium / RAB geranylgeranylation / 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 ...Anchoring of the basal body to the plasma membrane / VxPx cargo-targeting to cilium / RAB geranylgeranylation / 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 / kinetochore microtubule / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / exocytic vesicle / 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 / positive regulation of axon extension / 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 / endosome / axon / protein domain specific binding / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Pasqualato, S. / Senic-Matuglia, F. / Renault, L. / Goud, B. / Salamero, J. / Cherfils, J. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Crystallographic Evidence for Substrate-Assisted GTP Hydrolysis by a Small GTP Binding Protein Authors: Pasqualato, S. / Cherfils, J. #1: Journal: J.Biol.Chem. / Year: 2004 Title: The Structural Gdp/GTP Cycle of Rab11 Reveals a Novel Interface Involved in the Dynamics of Recycling Endosomes Authors: Pasqualato, S. / Senic-Matuglia, F. / Renault, L. / Goud, B. / Salamero, J. / Cherfils, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oix.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oix.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oix ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oix | HTTPS FTP |
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-Related structure data
Related structure data | 1oiwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21525.260 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-173 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DELETION MUTANT LACKING THE 43 C-TERMINAL RESIDUES / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24410, UniProt: P62491*PLUS |
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-Non-polymers , 5 types, 167 molecules
#2: Chemical | ChemComp-GDP / |
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#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEEREDSequence details | RESIDUES OF THE N-TERMINAL HIS6-TAG AND LINKER WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON ...RESIDUES OF THE N-TERMINAL HIS6-TAG AND LINKER WERE DISORDERED | |
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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: 1.99 Å3/Da / Density % sol: 38.19 % |
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Crystal grow | pH: 6.5 Details: 1.4 M NACL, 0.15 M NAH2PO4, 0.15 M KH2PO4,0.1 M NAMES PH6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 9, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 19517 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.279 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OIW Resolution: 1.7→30 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 Details: FINAL ROUND OF REFINEMENT WAS CARRIED OUT WITH REFMAC
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.052 Å2 / ksol: 0.373497 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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