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Yorodumi- PDB-2gzh: Crystal Structure of Rab11 in Complex with Rab11-Family Interacti... -
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-Basic information
Entry | Database: PDB / ID: 2gzh | ||||||
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Title | Crystal Structure of Rab11 in Complex with Rab11-Family Interacting Protein 2 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Ras-like G protein fold / a-helical coiled coil | ||||||
Function / homology | Function and homology information TRAM-dependent toll-like receptor 4 signaling pathway / 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 ...TRAM-dependent toll-like receptor 4 signaling pathway / 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 / regulated exocytosis / melanosome transport / amyloid-beta clearance by transcytosis / protein transmembrane transport / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / multivesicular body assembly / protein localization to cilium / dynein light intermediate chain binding / establishment of protein localization to membrane / protein localization to cell surface / insulin secretion involved in cellular response to glucose stimulus / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / establishment of cell polarity / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / phagocytic cup / centriolar satellite / mitotic spindle assembly / phagocytosis / vesicle-mediated transport / transport vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / phagocytic vesicle / multivesicular body / small monomeric GTPase / positive regulation of GTPase activity / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / cell projection / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of protein localization to plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / endosome / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / protein kinase binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 Å | ||||||
Authors | Khan, A.R. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Crystal structure of rab11 in complex with rab11 family interacting protein 2. Authors: Jagoe, W.N. / Lindsay, A.J. / Read, R.J. / McCoy, A.J. / McCaffrey, M.W. / Khan, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gzh.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gzh.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gzh_validation.pdf.gz | 738.9 KB | Display | wwPDB validaton report |
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Full document | 2gzh_full_validation.pdf.gz | 745.2 KB | Display | |
Data in XML | 2gzh_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 2gzh_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/2gzh ftp://data.pdbj.org/pub/pdb/validation_reports/gz/2gzh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological unit is generated by the crystallographic 2-fold axis, transformation (1,-1,-1). |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 19547.830 Da / Num. of mol.: 1 / Fragment: G protein domain / Mutation: Q70L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11a / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62491, small monomeric GTPase |
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#2: Protein | Mass: 12336.811 Da / Num. of mol.: 1 / Fragment: Rab11-FIP2 Rab-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMAL-c2x / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7L804 |
-Non-polymers , 4 types, 129 molecules
#3: Chemical | ChemComp-PO4 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GTP / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5 Details: Ammonium phosphate buffer, approximately 0.3M concentration, pH 5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98175 Å |
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2005 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98175 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→50 Å / Num. all: 10254 / Num. obs: 10234 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 16 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.47→2.56 Å / Redundancy: 10 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 15.9 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.47→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.799 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.29 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.639 Å2
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Refine analyze | Luzzati coordinate error free: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.47→2.536 Å / Total num. of bins used: 20
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