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- PDB-5szj: Structure of human Rab10 in complex with the bMERB domain of Mical-cL -
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Open data
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Basic information
Entry | Database: PDB / ID: 5szj | |||||||||
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Title | Structure of human Rab10 in complex with the bMERB domain of Mical-cL | |||||||||
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![]() | ENDOCYTOSIS / Mical-cL / DUF3585 / Mical / Rab effector / Rab10 | |||||||||
Function / homology | ![]() establishment of protein localization to endoplasmic reticulum membrane / endoplasmic reticulum tubular network organization / protein localization to basolateral plasma membrane / establishment of neuroblast polarity / F-actin monooxygenase / sulfur oxidation / endoplasmic reticulum tubular network / insulin-responsive compartment / regulated exocytosis / NAD(P)H oxidase H2O2-forming activity ...establishment of protein localization to endoplasmic reticulum membrane / endoplasmic reticulum tubular network organization / protein localization to basolateral plasma membrane / establishment of neuroblast polarity / F-actin monooxygenase / sulfur oxidation / endoplasmic reticulum tubular network / insulin-responsive compartment / regulated exocytosis / NAD(P)H oxidase H2O2-forming activity / polarized epithelial cell differentiation / 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 / exocytic vesicle / cadherin binding involved in cell-cell adhesion / Golgi to plasma membrane transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / RAB GEFs exchange GTP for GDP on RABs / actin filament depolymerization / establishment of protein localization to membrane / mitogen-activated protein kinase binding / endosomal transport / heart looping / antigen processing and presentation / vesicle-mediated transport / cytoskeleton organization / monooxygenase activity / FAD binding / axonogenesis / small monomeric GTPase / secretory granule membrane / G protein activity / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / adherens junction / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / cilium / recycling endosome membrane / cellular response to insulin stimulus / phagocytic vesicle membrane / GDP binding / actin binding / heart development / oxidoreductase activity / cytoskeleton / endosome membrane / endosome / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Mueller, M.P. / Gazdag, E.M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.1 KB | Display | ![]() |
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PDB format | ![]() | 116.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 767.5 KB | Display | ![]() |
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Full document | ![]() | 769.3 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lpnC ![]() 5szgSC ![]() 5szhC ![]() 5sziC ![]() 5szkC ![]() 4lhwS 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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1 |
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 22769.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 42 molecules ![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GNP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-PEG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18%-22% PEG 3350 0.2-0.3 M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→48.19 Å / Num. obs: 15861 / % possible obs: 99.96 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.137 / Rsym value: 0.143 / Net I/σ(I): 12.06 |
Reflection shell | Resolution: 2.66→2.7 Å / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.35 / CC1/2: 0.591 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LHW, 5SZG Resolution: 2.66→48.19 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.93 / 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: 2.66→48.19 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: 25.8237 Å / Origin y: 23.8064 Å / Origin z: -30.851 Å
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Refinement TLS group | Selection details: all |