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Yorodumi- PDB-1oiw: X-ray structure of the small G protein Rab11a in complex with GTP... -
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-Basic information
Entry | Database: PDB / ID: 1oiw | ||||||
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Title | X-ray structure of the small G protein Rab11a in complex with GTPgammaS | ||||||
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 / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle ...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 / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / regulation of cilium assembly / exosomal secretion / melanosome transport / amyloid-beta clearance by transcytosis / kinetochore microtubule / astral microtubule organization / VxPx cargo-targeting to cilium / protein transmembrane transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / exocytic vesicle / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / multivesicular body assembly / dynein light intermediate chain binding / protein localization to cilium / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / positive regulation of axon extension / transport vesicle / vesicle-mediated transport / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / centriole / multivesicular body / small monomeric GTPase / G protein activity / regulation of cytokinesis / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / endosome / protein domain specific binding / Golgi membrane / axon / 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: 2.05 Å | ||||||
Authors | Pasqualato, S. / Senic-Matuglia, F. / Renault, L. / Goud, B. / Salamero, J. / Cherfils, J. | ||||||
Citation | 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 | 1oiw.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oiw.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 1oiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oiw_validation.pdf.gz | 770 KB | Display | wwPDB validaton report |
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Full document | 1oiw_full_validation.pdf.gz | 776 KB | Display | |
Data in XML | 1oiw_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1oiw_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oiw ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oiw | HTTPS FTP |
-Related structure data
Related structure data | 1oivSC S: Starting model for refinement C: citing same article (ref.) |
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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
#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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#2: Chemical | ChemComp-GSP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.73 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Date: May 17, 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: 1.9→30 Å / Num. obs: 13509 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 22.16 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 14 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 9.35 / % possible all: 81.6 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 13984 / Num. measured all: 207365 / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 81.6 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 9.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OIV Resolution: 2.05→30 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES OF THE N-TERMINAL HIS6-TAG AND LINKER WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAP, AS WELL AS THE FIRST 7 RESIDUES OF RAB11A
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.7339 Å2 / ksol: 0.408489 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. reflection obs: 8007 / Num. reflection Rfree: 638 / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.323 / Rfactor Rwork: 0.248 |