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- PDB-5osi: Structure of retromer VPS29-VPS35C subunits complexed with RidL h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5osi | ||||||||||||
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Title | Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) | ||||||||||||
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![]() | TRANSPORT PROTEIN / Retromer / Legionella pneumophila | ||||||||||||
Function / homology | ![]() positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion ...positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion / regulation of terminal button organization / retromer, cargo-selective complex / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / negative regulation of late endosome to lysosome transport / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / retromer complex / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / dopaminergic synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of synapse maturation / voluntary musculoskeletal movement / regulation of protein metabolic process / transcytosis / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / regulation of mitochondrion organization / positive regulation of mitochondrial fission / lysosome organization / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / intracellular protein transport / protein destabilization / modulation of chemical synaptic transmission / regulation of protein stability / Wnt signaling pathway / negative regulation of inflammatory response / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / presynapse / postsynaptic density / lysosome / early endosome / endosome membrane / endosome / neuron projection / lysosomal membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / perinuclear region of cytoplasm / extracellular exosome / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Romano-Moreno, M. / Rojas, A.L. / Lucas, M. / Isupov, M.N. / Hierro, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL. Authors: Romano-Moreno, M. / Rojas, A.L. / Williamson, C.D. / Gershlick, D.C. / Lucas, M. / Isupov, M.N. / Bonifacino, J.S. / Machner, M.P. / Hierro, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 393.2 KB | Display | ![]() |
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PDB format | ![]() | 321.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.9 KB | Display | ![]() |
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Full document | ![]() | 527.2 KB | Display | |
Data in XML | ![]() | 65.9 KB | Display | |
Data in CIF | ![]() | 91.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oshC ![]() 5ot4C ![]() 2r17S S: Starting model for refinement C: citing same article ( |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Vacuolar protein sorting-associated protein ... , 2 types, 8 molecules ADGJBEHK
#1: Protein | Mass: 20531.705 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 35834.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 3 molecules CFI
#3: Protein/peptide | Mass: 1602.824 Da / Num. of mol.: 3 / Fragment: UNP residues 163-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lp12_2303 / Production host: ![]() ![]() |
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-Non-polymers , 3 types, 241 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2017 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.52→126.49 Å / Num. obs: 68126 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 39.897 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.155 / Net I/σ(I): 8.5 / Num. measured all: 425544 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.1 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2R17 Resolution: 2.52→126.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 13.251 / SU ML: 0.279 / SU R Cruickshank DPI: 2.3903 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.39 / ESU R Free: 0.341 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.99 Å2 / Biso mean: 52.082 Å2 / Biso min: 15.5 Å2
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Refinement step | Cycle: final / Resolution: 2.52→126.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.585 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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