+Open data
-Basic information
Entry | Database: PDB / ID: 4c4p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Wild-Type Rab11 Complexed to FIP2 | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / EFFECTOR / VESICLE TRAFFICKING / ENDOSOMES | ||||||
Function / homology | Function and homology information TRAM-dependent toll-like receptor 4 signaling pathway / 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 / establishment of vesicle localization / plasma membrane to endosome transport / regulation of cilium assembly ...TRAM-dependent toll-like receptor 4 signaling pathway / 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 / establishment of vesicle localization / plasma membrane to endosome transport / regulation of cilium assembly / regulated exocytosis / exosomal secretion / amyloid-beta clearance by transcytosis / melanosome 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 / protein localization to cilium / multivesicular body assembly / dynein light intermediate chain binding / establishment of protein localization to membrane / protein localization to cell surface / insulin secretion involved in cellular response to glucose stimulus / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / establishment of cell polarity / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / phagocytic cup / centriolar satellite / mitotic spindle assembly / phagocytosis / vesicle-mediated transport / transport vesicle / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / small monomeric GTPase / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / cell projection / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / small GTPase binding / positive regulation of GTPase activity / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / endosome / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / protein kinase binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å | ||||||
Authors | Sultana, A. / Khan, A.R. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Structural and Functional Analysis of Fip2 Binding to the Endosome-Localised Rab25 Gtpase Authors: Lall, P. / Horgan, C.P. / Oda, S. / Franklin, E. / Sultana, A. / Hanscomb, S.R. / Mccaffrey, M.W. / Khan, A.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4c4p.cif.gz | 155 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4c4p.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 4c4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/4c4p ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c4p | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19515.906 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-173 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62491 |
---|---|
#2: Protein | Mass: 12289.915 Da / Num. of mol.: 1 / Fragment: RAB-BINDING DOMAIN, RESIDUES 410-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7L804 |
#3: Chemical | ChemComp-GNP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Sequence details | N-TERMINALLY AND C-TERMINALLY TRUNCATED RAB11A, WITH A FEW NON-NATIVE RESIDUES AT N-TERMINUS FROM ...N-TERMINALLY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 18989 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.7 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2→27.955 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 19.53 / 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: 2→27.955 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 26.9827 Å / Origin y: 8.3308 Å / Origin z: 21.774 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |