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Yorodumi- PDB-2d7c: Crystal structure of human Rab11 in complex with FIP3 Rab-binding... -
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-Basic information
Entry | Database: PDB / ID: 2d7c | ||||||
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Title | Crystal structure of human Rab11 in complex with FIP3 Rab-binding domain | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / GTP-ase / coiled-coil / Structural Genomics | ||||||
Function / homology | Function and homology information postsynaptic recycling endosome membrane / 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 / negative regulation of adiponectin secretion ...postsynaptic recycling endosome membrane / 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 / negative regulation of adiponectin secretion / 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 / endocytic recycling / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / intercellular bridge / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / endocytic vesicle / centriolar satellite / mitotic spindle assembly / 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 / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / neuron projection development / endocytic vesicle membrane / midbody / cytoplasmic vesicle / microtubule binding / vesicle / molecular adaptor activity / endosome / cell cycle / cell division / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / calcium ion binding / protein-containing complex binding / GTP binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Shiba, T. / Koga, H. / Shin, H.W. / Kawasaki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1. Authors: Shiba, T. / Koga, H. / Shin, H.W. / Kawasaki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d7c.cif.gz | 104.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d7c.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 2d7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/2d7c ftp://data.pdbj.org/pub/pdb/validation_reports/d7/2d7c | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 18871.107 Da / Num. of mol.: 2 / Fragment: residues 7-173 / Mutation: Q70L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62491 #2: Protein/peptide | Mass: 5090.523 Da / Num. of mol.: 2 / Fragment: Rab-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O75154 |
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-Non-polymers , 4 types, 415 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% iso-propanol, 3% (w/v) PEG 4000, 0.05M MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.75→50 Å / Num. all: 49404 / Num. obs: 49356 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3 | ||||||||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 1.75→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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