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Open data
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Basic information
Entry | Database: PDB / ID: 4uj4 | ||||||
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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 / RABIN8 / RAB11 / FIP3 | ||||||
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 / dynein light intermediate chain binding / protein localization to cilium / 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 / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / protein transport / GTPase binding / lamellipodium / 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 | ||||||
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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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 609.5 KB | Display | ![]() |
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PDB format | ![]() | 504.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 60.8 KB | Display | |
Data in CIF | ![]() | 79.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uj3SC ![]() 4uj5C S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 20958.578 Da / Num. of mol.: 4 / Fragment: GTPASE DOMAIN, RESIDUES 4-186 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 22217.479 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 286-476 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 7269.180 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 695-756 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-GNP / #5: Chemical | ChemComp-MG / Sequence details | Q70L POINT MUTATION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 5.8 Details: 50MM MES PH 5.8, 0.2M AMMONIUM SULFATE AND 14% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / 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: 4.2→50 Å / Num. obs: 15003 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 149.24 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11 |
Reflection shell | Resolution: 4.2→4.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.6 / % possible all: 61 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4UJ3 Resolution: 4.2→49.469 Å / SU ML: 0.51 / σ(F): 1.35 / Phase error: 29.73 / 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: 4.2→49.469 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.7022 Å / Origin y: -25.0956 Å / Origin z: -39.0344 Å
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Refinement TLS group | Selection details: ALL |