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- PDB-6ekk: Crystal structure of GEF domain of DENND 1A in complex with Rab G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ekk | ||||||
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Title | Crystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound state. | ||||||
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![]() | TRANSCRIPTION / DENND1A- DENN domain-containing protein 1A RAB35- Ras-related protein Rab-35 | ||||||
Function / homology | ![]() regulation of Rab protein signal transduction / Rab protein signal transduction / plasma membrane to endosome transport / phosphatidylinositol phosphate binding / protein localization to endosome / clathrin-coated vesicle membrane / cell projection membrane / clathrin-coated endocytic vesicle / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs ...regulation of Rab protein signal transduction / Rab protein signal transduction / plasma membrane to endosome transport / phosphatidylinositol phosphate binding / protein localization to endosome / clathrin-coated vesicle membrane / cell projection membrane / clathrin-coated endocytic vesicle / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / phosphatidylinositol-3-phosphate binding / endocytic recycling / TBC/RABGAPs / clathrin-coated vesicle / endosomal transport / intercellular bridge / antigen processing and presentation / synaptic vesicle endocytosis / mitotic cytokinesis / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / clathrin-coated endocytic vesicle membrane / protein localization / small GTPase binding / SH3 domain binding / endocytosis / recycling endosome membrane / GDP binding / neuron projection development / melanosome / protein transport / presynaptic membrane / endosome membrane / intracellular membrane-bounded organelle / GTPase activity / neuronal cell body / dendrite / GTP binding / extracellular exosome / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Srikannathasan, V. / Szykowska, A. / Tallant, C. / Strain-Damerell, C. / Kopec, J. / Kupinska, K. / Mukhopadhyay, S. / Gavin, M. / Wang, D. / Chalk, R. ...Srikannathasan, V. / Szykowska, A. / Tallant, C. / Strain-Damerell, C. / Kopec, J. / Kupinska, K. / Mukhopadhyay, S. / Gavin, M. / Wang, D. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Huber, K. | ||||||
![]() | ![]() Title: Crystal structure of DENND1A-RAB35 complex with GDP bound state. Authors: Srikannathasan, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 483.3 KB | Display | ![]() |
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PDB format | ![]() | 392.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 49.4 KB | Display | |
Data in CIF | ![]() | 72.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tw8S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 45006.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chain A- DENND1AA (UNIPROT Q8TEH3) Chain B- RAB35 (UNIPROT - Q15286) Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 20077.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 879 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25%PEG3350, 0.2M AMS, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2017 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50.452 Å / Num. obs: 115286 / % possible obs: 95.7 % / Redundancy: 3.4 % / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.82→1.87 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TW8 Resolution: 1.82→50.452 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 26.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.5 Å2 / Biso mean: 36.0058 Å2 / Biso min: 17.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.82→50.452 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Origin x: 17.726 Å / Origin y: 9.6475 Å / Origin z: 25.363 Å
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Refinement TLS group |
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