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Open data
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Basic information
Entry | Database: PDB / ID: 2bme | ||||||
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Title | high resolution structure of GppNHp-bound human Rab4a | ||||||
![]() | RAS-RELATED PROTEIN RAB4A | ||||||
![]() | PROTEIN TRANSPORT / GTP-BINDING PROTEIN / VESICULAR TRANSPORT / ENDOCYTOSIS / PRENYLATION / TRANSPORT | ||||||
Function / homology | ![]() postsynaptic recycling endosome / Rab protein signal transduction / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / antigen processing and presentation / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / vesicle-mediated transport ...postsynaptic recycling endosome / Rab protein signal transduction / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / antigen processing and presentation / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / vesicle-mediated transport / small monomeric GTPase / G protein activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / recycling endosome membrane / GDP binding / protein transport / early endosome membrane / vesicle / GTPase activity / GTP binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scheidig, A.J. / Huber, S.K. | ||||||
![]() | ![]() Title: High Resolution Crystal Structures of Human Rab4A in its Active and Inactive Conformations. Authors: Huber, S.K. / Scheidig, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.1 KB | Display | ![]() |
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PDB format | ![]() | 136 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bmdC ![]() 1huqS C: citing same article ( S: Starting model for refinement |
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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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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 20990.775 Da / Num. of mol.: 4 / Fragment: NUCLEOTIDE-BINDING DOMAIN, RESIDUES 1-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 698 molecules ![](data/chem/img/GNP.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GNP / #3: Chemical | ChemComp-TRS / #4: Chemical | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.24 % Description: USED MODEL WITHOUT NUCLEOTIDE, MAGNESIUM AND WATER |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 8% (W/V) PEG 4000, 100MM SODIUM ACETATE PH 4.0 HANGING DROP 25 DEGREE CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 23, 2002 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 128819 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.6→1.75 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6.7 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HUQ Resolution: 1.57→19.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.634 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→19.54 Å
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Refine LS restraints |
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