[English] 日本語
Yorodumi- PDB-4hlq: Crystal structure of human rab1b bound to GDP and BEF3 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hlq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens | ||||||
Components |
| ||||||
Keywords | HYDROLASE ACTIVATOR/PROTEIN TRANSPORT / Rab1b / RabGAP / Fluorides / GTPase-Activating Proteins / rab GTP-Binding Proteins / HYDROLASE ACTIVATOR-PROTEIN TRANSPORT complex | ||||||
Function / homology | Function and homology information positive regulation of glycoprotein metabolic process / acrosome assembly / positive regulation of ER to Golgi vesicle-mediated transport / positive regulation by host of viral genome replication / COPII-coated vesicle cargo loading / lens fiber cell morphogenesis / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / 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 / positive regulation by host of viral genome replication / COPII-coated vesicle cargo loading / lens fiber cell morphogenesis / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / positive regulation by virus of viral protein levels in host cell / lipid droplet organization / 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 / virion assembly / seminiferous tubule development / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / small monomeric GTPase / G protein activity / intracellular protein transport / small GTPase binding / positive regulation of GTPase activity / nuclear membrane / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Gazdag, E.M. / Gavriljuk, K. / Itzen, A. / Koetting, C. / Gerwert, K. / Goody, R.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hlq.cif.gz | 875.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hlq.ent.gz | 732.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/4hlq ftp://data.pdbj.org/pub/pdb/validation_reports/hl/4hlq | HTTPS FTP |
---|
-Related structure data
Related structure data | 4hl4SC 3nkvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: TBC1D20, C20orf140 / Plasmid: pOPINM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q96BZ9 #2: Protein | Mass: 19752.369 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9H0U4 |
---|
-Non-polymers , 5 types, 71 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GDP / #6: Chemical | ChemComp-BEF / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.65 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→49.22 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|