+Open data
-Basic information
Entry | Database: PDB / ID: 4uj3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human Rab11-Rabin8-FIP3 | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN / CILIARY TARGETING COMPLEX / CILIUM / VESICULAR TRANSPORT / MEMBRANE TRAFFICKING | ||||||
Function / homology | Function and homology information postsynaptic recycling endosome membrane / Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / 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 / protein localization to organelle ...postsynaptic recycling endosome membrane / Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / 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 / protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / negative regulation of filopodium assembly / negative regulation of adiponectin secretion / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / melanosome 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 / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / multivesicular body assembly / 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 / endocytic vesicle / cilium assembly / 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 / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / trans-Golgi network membrane / ciliary basal body / 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 / protein transport / GTPase binding / lamellipodium / 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 / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Vetter, M. / Lorentzen, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4uj3.cif.gz | 598.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4uj3.ent.gz | 481.5 KB | Display | PDB format |
PDBx/mmJSON format | 4uj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/4uj3 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/4uj3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4uj4C 4uj5C 1yzkS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
5 |
| ||||||||||||
6 |
| ||||||||||||
7 |
| ||||||||||||
8 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|
-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.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62491 #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.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96QF0 #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.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75154 |
---|
-Non-polymers , 5 types, 126 molecules
#4: Chemical | ChemComp-GNP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|