+Open data
-Basic information
Entry | Database: PDB / ID: 6iy1 | ||||||
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Title | Structure of human Ras-related protein Rab11 | ||||||
Components | (Ras-related protein Rab-11A) x 3 | ||||||
Keywords | TRANSPORT PROTEIN / Complex / transport / GTPase | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / 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 / mitotic spindle assembly / centriolar satellite / 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 / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / Golgi apparatus / protein-containing complex / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Ma, P. / Li, S. / Li, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of human Ras-related protein Rab11 Authors: Ma, P. / Li, S. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iy1.cif.gz | 211.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iy1.ent.gz | 168.1 KB | Display | PDB format |
PDBx/mmJSON format | 6iy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/6iy1 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/6iy1 | HTTPS FTP |
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-Related structure data
Related structure data | 1oivS 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
#1: Protein | Mass: 18546.895 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491 #2: Protein | | Mass: 18839.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491 #3: Protein | | Mass: 18954.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GDP / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491 #4: Chemical | ChemComp-GDP / #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: 40.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.15M Li2SO4, 0.1M Glycine, 0.8M NaH2PO4 1.2M Na2HPO4 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 48648 / % possible obs: 91.2 % / Redundancy: 2.5 % / CC1/2: 0.945 / Rpim(I) all: 0.063 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 2190 / CC1/2: 0.945 / Rpim(I) all: 0.248 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OIV Resolution: 2.11→46.73 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.243
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.154 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→46.73 Å
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