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Yorodumi- PDB-1oiv: X-ray structure of the small G protein Rab11a in complex with GDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oiv | ||||||
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Title | X-ray structure of the small G protein Rab11a in complex with GDP | ||||||
Components | RAS-RELATED PROTEIN RAB-11A | ||||||
Keywords | PROTEIN TRANSPORT / SMALL G PROTEIN / INTRACELLULAR TRAFFICKING / GTP-BINDING / LIPOPROTEIN | ||||||
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: 1.98 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 | 1oiv.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oiv.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oiv_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1oiv_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1oiv_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1oiv_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oiv ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oiv | HTTPS FTP |
-Related structure data
Related structure data | 1oiwC 1g16S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.31774, -0.90002, 0.29833), Vector: Details | THIS MAY BE RESULT OF CRYSTAL PACKING | |
-Components
#1: Protein | Mass: 21540.230 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-173 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 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-EDO / | #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: 2.07 Å3/Da / Density % sol: 40.69 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 1.7M (NH4)2SO4,5%PEG400,8% 1,3 BUTANEDIOL,0.1M TRIS-HCL PH8.0, pH 8.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / PH range low: 8.5 / PH range high: 8 | ||||||||||||||||||||||||||||||||||||
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: ID14-1 / Wavelength: 0.934 |
Detector | Date: Nov 11, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 26143 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.393 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. obs: 26100 / Num. measured all: 233617 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G16 Resolution: 1.98→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1189171.58 / 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 5 RESIDUES OF RAB11A. ASP6 WAS MODELLED AS ALANINE BECAUSE ...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 5 RESIDUES OF RAB11A. ASP6 WAS MODELLED AS ALANINE BECAUSE ITS SIDE CHAIN WAS NOT VISIBLE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.7544 Å2 / ksol: 0.399156 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.98→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.03 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 15
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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