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Yorodumi- PDB-5lpn: Structure of human Rab10 in complex with the bMERB domain of Mical-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lpn | |||||||||
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Title | Structure of human Rab10 in complex with the bMERB domain of Mical-1 | |||||||||
Components |
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Keywords | ENDOCYTOSIS / Mical-1 / DUF3585 / Mical / Rab effector / Rab10 / oxidoreductase | |||||||||
Function / homology | Function and homology information endoplasmic reticulum tubular network organization / protein localization to basolateral plasma membrane / establishment of protein localization to endoplasmic reticulum membrane / establishment of neuroblast polarity / hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / secretory vesicle / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation ...endoplasmic reticulum tubular network organization / protein localization to basolateral plasma membrane / establishment of protein localization to endoplasmic reticulum membrane / establishment of neuroblast polarity / hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / secretory vesicle / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / endoplasmic reticulum tubular network / regulation of regulated secretory pathway / insulin-responsive compartment / regulated exocytosis / NAD(P)H oxidase H2O2-forming activity / polarized epithelial cell differentiation / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / exocytic vesicle / cadherin binding involved in cell-cell adhesion / RAB geranylgeranylation / Golgi to plasma membrane transport / myosin V binding / Golgi to plasma membrane protein transport / RAB GEFs exchange GTP for GDP on RABs / actin filament depolymerization / establishment of protein localization to membrane / intermediate filament / endosomal transport / intercellular bridge / exocytosis / actin filament bundle assembly / antigen processing and presentation / protein secretion / vesicle-mediated transport / cytoskeleton organization / monooxygenase activity / FAD binding / axonogenesis / small monomeric GTPase / secretory granule membrane / G protein activity / negative regulation of protein phosphorylation / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / adherens junction / trans-Golgi network / cytoplasmic vesicle membrane / cellular response to insulin stimulus / recycling endosome / cilium / small GTPase binding / SH3 domain binding / actin filament binding / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / actin binding / midbody / endosome / endosome membrane / cytoskeleton / Golgi membrane / focal adhesion / endoplasmic reticulum membrane / Neutrophil degranulation / negative regulation of apoptotic process / GTP binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Mueller, M.P. / Gazdag, E.M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Elife / Year: 2016 Title: bMERB domains are bivalent Rab8 family effectors evolved by gene duplication. Authors: Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Gazdag, E.M. / Muller, M.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lpn.cif.gz | 208.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lpn.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lpn_validation.pdf.gz | 1010.2 KB | Display | wwPDB validaton report |
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Full document | 5lpn_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5lpn_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5lpn_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/5lpn ftp://data.pdbj.org/pub/pdb/validation_reports/lp/5lpn | HTTPS FTP |
-Related structure data
Related structure data | 5szgSC 5szhC 5sziC 5szjC 5szkC 4lhwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20202.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB10 / Production host: Escherichia coli (E. coli) / References: UniProt: P61026 #2: Protein | | Mass: 17852.303 Da / Num. of mol.: 1 / Fragment: UNP residues 918-1067 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MICAL1, MICAL, NICAL / Production host: Escherichia coli (E. coli) References: UniProt: Q8TDZ2, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 6%-10% PEG8000 0.1M Imidazole / PH range: 7.6-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2015 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→44.004 Å / Num. obs: 17508 / % possible obs: 99.63 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.118 / Rsym value: 0.123 / Net I/σ(I): 14.12 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 3.25 / CC1/2: 0.803 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4lhw and 5szg Resolution: 2.8→44.004 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→44.004 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.7086 Å / Origin y: 73.9068 Å / Origin z: 216.9504 Å
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Refinement TLS group | Selection details: all |