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Open data
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Basic information
Entry | Database: PDB / ID: 2bcg | ||||||
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Title | Structure of doubly prenylated Ypt1:GDI complex | ||||||
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Function / homology | ![]() pre-mRNA catabolic process / Rab GDP-dissociation inhibitor activity / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport ...pre-mRNA catabolic process / Rab GDP-dissociation inhibitor activity / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / COPII-coated vesicle budding / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to phagophore assembly site / phagophore assembly site membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pylypenko, O. / Rak, A. / Alexandrov, K. | ||||||
![]() | ![]() Title: Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling Authors: Pylypenko, O. / Rak, A. / Durek, T. / Kushnir, S. / Dursina, B.E. / Thomae, N.H. / Constantinescu, A.T. / Brunsveld, L. / Watzke, A. / Waldmann, H. / Goody, R.S. / Alexandrov, K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.6 KB | Display | ![]() |
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PDB format | ![]() | 252.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ukvS 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules GY
#1: Protein | Mass: 51466.430 Da / Num. of mol.: 1 / Fragment: RabGDI Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: GDI1 / Plasmid: pET19 / Species (production host): Escherichia coli / Production host: ![]() ![]() ![]() |
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#2: Protein | Mass: 23286.318 Da / Num. of mol.: 1 / Fragment: YPT1 / Mutation: G204C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: YPT1 / Plasmid: pTWIN-1 / Species (production host): Escherichia coli / Production host: ![]() ![]() ![]() |
-Non-polymers , 5 types, 928 molecules ![](data/chem/img/GER.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-GDP / | ![]() #6: Chemical | ChemComp-TRS / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 14% PEG MME 2000, 100 mM Tris-Acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.48→19.92 Å / Num. all: 113100 / Num. obs: 109178 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 24 Å2 / Rsym value: 0.076 / Net I/σ(I): 11.32 |
Reflection shell | Resolution: 1.48→1.49 Å / % possible all: 75.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1ukv Resolution: 1.48→19.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.609 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.071 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.48→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.518 Å / Total num. of bins used: 20 /
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