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Open data
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Basic information
Entry | Database: PDB / ID: 5f0j | ||||||||||||
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Title | Structure of retromer VPS26-VPS35 subunits bound to SNX3 | ||||||||||||
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Function / homology | ![]() negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / protein to membrane docking / negative regulation of protein transport / 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 / membrane invagination ...negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / protein to membrane docking / negative regulation of protein transport / 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 / membrane invagination / negative regulation of protein homooligomerization / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Lucas, M. / Gershlick, D. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Mechanism for Cargo Recognition by the Retromer Complex. Authors: Lucas, M. / Gershlick, D.C. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / 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 | ![]() | 209.1 KB | Display | ![]() |
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PDB format | ![]() | 162.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5f0kC ![]() 5f0lC ![]() 5f0mC ![]() 5f0pC ![]() 2fauS ![]() 2ypsS 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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Unit cell |
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Components
-Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 53288.270 Da / Num. of mol.: 1 / Fragment: Residues 14-470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 40239.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Protein , 1 types, 1 molecules C
#3: Protein | ![]() Mass: 19193.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 130 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / ![]() #5: Chemical | ChemComp-GOL / ![]() #6: Chemical | ChemComp-EDO / ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.46 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.9 M AmSO4, 0.1 M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.69→57 Å / Num. obs: 85401 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 67.063 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.107 / Χ2: 1.064 / Net I/σ(I): 12.09 / Num. measured all: 292428 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2FAU, 2YPS Resolution: 2.7→56.98 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.2072 / FOM work R set: 0.8343 / SU B: 11.486 / SU ML: 0.224 / SU R Cruickshank DPI: 0.5345 / SU Rfree: 0.3016 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.07 Å2 / Biso mean: 57.454 Å2 / Biso min: 16.35 Å2
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Refinement step | Cycle: final / Resolution: 2.7→56.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.698→2.768 Å / Total num. of bins used: 20
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