[English] 日本語
Yorodumi- PDB-6ekk: Crystal structure of GEF domain of DENND 1A in complex with Rab G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ekk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound state. | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / DENND1A- DENN domain-containing protein 1A RAB35- Ras-related protein Rab-35 | ||||||
Function / homology | Function and homology information 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 / synaptic vesicle endocytosis / mitotic cytokinesis / antigen processing and presentation / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / cellular response to nerve growth factor stimulus / clathrin-coated endocytic vesicle membrane / protein localization / small GTPase binding / positive regulation of GTPase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: To be published Title: Crystal structure of DENND1A-RAB35 complex with GDP bound state. Authors: Srikannathasan, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ekk.cif.gz | 483.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ekk.ent.gz | 392.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ekk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6ekk ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6ekk | HTTPS FTP |
---|
-Related structure data
Related structure data | 3tw8S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: DENND1A, FAM31A, KIAA1608 / Plasmid: pFB-CT10HF-LIC / Details (production host): C-terminal TAg / Cell (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEH3 #2: Protein | Mass: 20077.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB35, RAB1C, RAY / Plasmid: pNIC28-Bsa4 / Details (production host): N-terminal his tag / Cell (production host): Escherichia Coli BL21 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15286 |
---|
-Non-polymers , 4 types, 879 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.49 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 17.726 Å / Origin y: 9.6475 Å / Origin z: 25.363 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|