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Yorodumi- PDB-5szi: Structure of human Rab8a in complex with the bMERB domain of Mical-cL -
+Open data
-Basic information
Entry | Database: PDB / ID: 5szi | |||||||||
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Title | Structure of human Rab8a in complex with the bMERB domain of Mical-cL | |||||||||
Components |
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Keywords | ENDOCYTOSIS / Mical-cL / DUF3585 / Mical / Rab effector / Rab8a / transport protein | |||||||||
Function / homology | Function and homology information F-actin monooxygenase / neurotransmitter receptor transport to postsynaptic membrane / sulfur oxidation / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / NAD(P)H oxidase H2O2-forming activity / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen ...F-actin monooxygenase / neurotransmitter receptor transport to postsynaptic membrane / sulfur oxidation / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / NAD(P)H oxidase H2O2-forming activity / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / trans-Golgi network transport vesicle / regulation of exocytosis / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / actin filament depolymerization / non-motile cilium / endocytic recycling / TBC/RABGAPs / mitogen-activated protein kinase binding / ciliary membrane / ciliary base / heart looping / Golgi organization / cilium assembly / protein secretion / phagocytic vesicle / cytoskeleton organization / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / centriole / FAD binding / axonogenesis / small monomeric GTPase / trans-Golgi network membrane / ciliary basal body / regulation of autophagy / actin filament / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / monooxygenase activity / regulation of long-term neuronal synaptic plasticity / cilium / small GTPase binding / autophagy / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / actin binding / heart development / midbody / dendritic spine / postsynaptic density / oxidoreductase activity / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Mueller, M.P. / Gazdag, E.M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Elife / Year: 2016 Title: bMERB domains are bivalent Rab8 family effectors evolved by gene duplication. Authors: Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Gazdag, E.M. / Muller, M.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5szi.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5szi.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 5szi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/5szi ftp://data.pdbj.org/pub/pdb/validation_reports/sz/5szi | HTTPS FTP |
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-Related structure data
Related structure data | 5lpnC 5szgSC 5szhC 5szjC 5szkC 4lhwS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23897.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli (E. coli) / References: UniProt: P61006 |
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#2: Protein | Mass: 18469.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MICALCL / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZW33 |
#3: Chemical | ChemComp-GNP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M bis tris propane 0.2M tri sodium citrate 20% PEG 3350 PH range: 8.3-8.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00009 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2015 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00009 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→46 Å / Num. obs: 12810 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.092 / Net I/σ(I): 16.45 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.507 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LHW, 5SZG Resolution: 2.85→45.952 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 30.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→45.952 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: 8.4498 Å / Origin y: 45.9171 Å / Origin z: -14.3057 Å
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Refinement TLS group | Selection details: (chain A and resseq 2:400) |