+Open data
-Basic information
Entry | Database: PDB / ID: 4uj4 | ||||||
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Title | Crystal structure of human Rab11-Rabin8-FIP3 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / CILIARY TARGETING COMPLEX / CILIUM / VESICULAR TRANSPORT / MEMBRANE TRAFFICKING / RABIN8 / RAB11 / FIP3 | ||||||
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: 4.2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uj4.cif.gz | 609.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uj4.ent.gz | 504.8 KB | Display | PDB format |
PDBx/mmJSON format | 4uj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/4uj4 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/4uj4 | HTTPS FTP |
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-Related structure data
Related structure data | 4uj3SC 4uj5C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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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.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Plasmid: PET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62491 #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.) Homo sapiens (human) / Gene: RAB3IP, RABIN8 / Plasmid: PET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96QF0 #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.) Homo sapiens (human) / Gene: RAB11FIP3, ARFO1, KIAA0665 / Plasmid: PET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75154 #4: Chemical | ChemComp-GNP / #5: Chemical | ChemComp-MG / Sequence details | Q70L POINT MUTATION | |
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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: 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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |