[English] 日本語

- PDB-5szk: Structure of human N-terminally engineered Rab1b in complex with ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5szk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human N-terminally engineered Rab1b in complex with the bMERB domain of Mical-cL | |||||||||
![]() |
| |||||||||
![]() | ENDOCYTOSIS / Mical-cL / DUF3585 / Mical / Rab effector / Rab1b / protein transport | |||||||||
Function / homology | ![]() positive regulation of glycoprotein metabolic process / F-actin monooxygenase / F-actin monooxygenase activity / sulfur oxidation / NAD(P)H oxidase H2O2-forming activity / 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 / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / actin filament depolymerization ...positive regulation of glycoprotein metabolic process / F-actin monooxygenase / F-actin monooxygenase activity / sulfur oxidation / NAD(P)H oxidase H2O2-forming activity / 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 / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / actin filament depolymerization / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / mitogen-activated protein kinase binding / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / heart looping / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport / cytoskeleton organization / endoplasmic reticulum-Golgi intermediate compartment membrane / endomembrane system / FAD binding / small monomeric GTPase / actin filament / intracellular protein transport / monooxygenase activity / actin binding / G protein activity / heart development / oxidoreductase activity / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Gazdag, E.M. / Mueller, M.P. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 147.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 116 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 766.8 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lpnC ![]() 5szgSC ![]() 5szhC ![]() 5sziC ![]() 5szjC ![]() 3nkvS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18469.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 22352.361 Da / Num. of mol.: 1 / Mutation: N2A, P3K, E4T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GNP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M bis-tris pH 7.5, 0.2M sodium malonate and 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2015 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91908 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→44.8 Å / Num. obs: 12904 / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.079 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.45 / CC1/2: 0.757 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3NKV, 5SZG Resolution: 2.8→44.8 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.44
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→44.8 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|