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- PDB-4hlq: Crystal structure of human rab1b bound to GDP and BEF3 in complex... -
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Basic information
Entry | Database: PDB / ID: 4hlq | ||||||
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Title | Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens | ||||||
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![]() | HYDROLASE ACTIVATOR/PROTEIN TRANSPORT / Rab1b / RabGAP / Fluorides / GTPase-Activating Proteins / rab GTP-Binding Proteins / HYDROLASE ACTIVATOR-PROTEIN TRANSPORT complex | ||||||
Function / homology | ![]() positive regulation of glycoprotein metabolic process / acrosome assembly / positive regulation of ER to Golgi vesicle-mediated transport / COPII-coated vesicle cargo loading / positive regulation by host of viral genome replication / lens fiber cell morphogenesis / RAB geranylgeranylation / phagophore assembly site membrane / lipid droplet organization / positive regulation by virus of viral protein levels in host cell ...positive regulation of glycoprotein metabolic process / acrosome assembly / positive regulation of ER to Golgi vesicle-mediated transport / COPII-coated vesicle cargo loading / positive regulation by host of viral genome replication / lens fiber cell morphogenesis / RAB geranylgeranylation / phagophore assembly site membrane / lipid droplet organization / positive regulation by virus of viral protein levels in host cell / regulation of autophagosome assembly / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / TBC/RABGAPs / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / seminiferous tubule development / virion assembly / Golgi organization / autophagosome assembly / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / small monomeric GTPase / G protein activity / positive regulation of GTPase activity / intracellular protein transport / small GTPase binding / nuclear membrane / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gazdag, E.M. / Gavriljuk, K. / Itzen, A. / Koetting, C. / Gerwert, K. / Goody, R.S. | ||||||
![]() | ![]() Title: Catalytic mechanism of a mammalian Rab-RabGAP complex in atomic detail. Authors: Gavriljuk, K. / Gazdag, E.M. / Itzen, A. / Kotting, C. / Goody, R.S. / Gerwert, K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 875.3 KB | Display | ![]() |
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PDB format | ![]() | 732.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4hl4SC ![]() 3nkvS 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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3 | ![]()
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5 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 10 molecules ACEGIBDFHJ
#1: Protein | Mass: 34963.113 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 19752.369 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 71 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GDP / #6: Chemical | ChemComp-BEF / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 1.6M ammonium sulphate, 0.1M Hepes pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2012 |
Radiation | Monochromator: SI(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 46667 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.63 % / Rmerge(I) obs: 0.0561 / Rsym value: 0.0695 / Net I/σ(I): 3.31 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 6.47 % / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HL4, 3NKV Resolution: 3.3→49.22 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.874 / SU B: 57.698 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.583 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.194 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→49.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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