+Open data
-Basic information
Entry | Database: PDB / ID: 6ixv | ||||||
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Title | Crystal structure of SH3BP5-Rab11a | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Rab11 / GEF / SH3BP5 | ||||||
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 / 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 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 / astral microtubule organization / VxPx cargo-targeting to cilium / protein transmembrane transport / 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 / 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 / protein kinase inhibitor activity / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / 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 / guanyl-nucleotide exchange factor 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 / SH3 domain binding / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / nuclear body / intracellular signal transduction / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / Golgi apparatus / signal transduction / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Goto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Life Sci Alliance / Year: 2019 Title: Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Authors: Goto-Ito, S. / Morooka, N. / Yamagata, A. / Sato, Y. / Sato, K. / Fukai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ixv.cif.gz | 322.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ixv.ent.gz | 261.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ixv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ixv_validation.pdf.gz | 485.1 KB | Display | wwPDB validaton report |
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Full document | 6ixv_full_validation.pdf.gz | 500.9 KB | Display | |
Data in XML | 6ixv_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 6ixv_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/6ixv ftp://data.pdbj.org/pub/pdb/validation_reports/ix/6ixv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31184.105 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SH3BP5, SAB / Production host: Escherichia coli (E. coli) / References: UniProt: O60239 #2: Protein | Mass: 19741.131 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 #3: Chemical | |
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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: 4.37 Å3/Da / Density % sol: 71.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.6M NaCl, 0.1M NaH2PO4 pH 6.8, 16% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 35583 / % possible obs: 100 % / Redundancy: 32.6 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 41.1 |
Reflection shell | Resolution: 3.8→3.87 Å / Rmerge(I) obs: 1.546 / Num. unique obs: 1505 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→49.769 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→49.769 Å
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Refine LS restraints |
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LS refinement shell |
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