+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ixv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SH3BP5-Rab11a | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / Rab11 / GEF / SH3BP5 | ||||||
Function / homology | ![]() 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 / 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 / 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 epithelial cell migration / protein kinase inhibitor activity / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / 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 / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 322.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 261.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 500.9 KB | Display | |
Data in XML | ![]() | 52.2 KB | Display | |
Data in CIF | ![]() | 69.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31184.105 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 19741.131 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.88 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|