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Open data
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Basic information
Entry | Database: PDB / ID: 4uj3 | ||||||
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Title | Crystal structure of human Rab11-Rabin8-FIP3 | ||||||
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![]() | TRANSPORT PROTEIN / CILIARY TARGETING COMPLEX / CILIUM / VESICULAR TRANSPORT / MEMBRANE TRAFFICKING | ||||||
Function / homology | ![]() postsynaptic recycling endosome membrane / Golgi to plasma membrane transport vesicle / protein localization to motile cilium / ciliary basal body-plasma membrane docking / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport ...postsynaptic recycling endosome membrane / Golgi to plasma membrane transport vesicle / protein localization to motile cilium / ciliary basal body-plasma membrane docking / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / 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 / protein localization to organelle / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / negative regulation of adiponectin secretion / regulation of cilium assembly / negative regulation of filopodium assembly / exosomal secretion / melanosome transport / amyloid-beta clearance by transcytosis / protein transmembrane transport / astral microtubule organization / proximal dendrite / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / BBSome-mediated cargo-targeting to cilium / regulation of vesicle-mediated transport / Golgi to plasma membrane transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / positive regulation of cilium assembly / RAB GEFs exchange GTP for GDP on RABs / multivesicular body assembly / protein localization to cilium / dynein light intermediate chain binding / endocytic recycling / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / protein targeting to membrane / syntaxin binding / mitotic metaphase chromosome alignment / intercellular bridge / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / endocytic vesicle / cilium 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 / ciliary basal body / 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 / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / protein transport / lamellipodium / GTPase binding / protein-macromolecule adaptor activity / 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 / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vetter, M. / Lorentzen, E. | ||||||
![]() | ![]() Title: Structure of Rab11-Fip3-Rabin8 Reveals Simultaneous Binding of Fip3 and Rabin8 Effectors to Rab11. Authors: Vetter, M. / Stehle, R. / Basquin, C. / Lorentzen, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 598.4 KB | Display | ![]() |
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PDB format | ![]() | 481.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 114.5 KB | Display | |
Data in CIF | ![]() | 147.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uj4C ![]() 4uj5C ![]() 1yzkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
-Protein , 3 types, 24 molecules ADGJMPSVBEHKNQTWCFILORUX
#1: Protein | Mass: 21116.736 Da / Num. of mol.: 8 / Fragment: GTPASE DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 22217.479 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 7269.180 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 126 molecules ![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GNP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 50MM MES PH 5.6, 0.2M AMMONIUM SULFATE AND 12% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 92398 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.97→3.14 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YZK Resolution: 3→48.543 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 27.83 / 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→48.543 Å
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Refine LS restraints |
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LS refinement shell |
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