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- PDB-6u3w: Crystal structure of yeast alpha/epsilon-COP of the COPI vesicula... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u3w | |||||||||
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Title | Crystal structure of yeast alpha/epsilon-COP of the COPI vesicular coat | |||||||||
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![]() | TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() vesicle coating / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding ...vesicle coating / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / promoter-specific chromatin binding / intracellular protein transport / protein transport / Golgi membrane / structural molecule activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Travis, S.M. / Hughson, F.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering. Authors: Travis, S.M. / Kokona, B. / Fairman, R. / Hughson, F.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.6 KB | Display | ![]() |
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PDB format | ![]() | 103.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tztC ![]() 6u3vC ![]() 3mv2S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 33985.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: COP1, RET1, SEC33, SOO1, YDL145C, D1578 / Plasmid: pETDuet-1 / Production host: ![]() ![]() |
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#2: Protein | Mass: 35474.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SEC28, YIL076W / Plasmid: pETDuet-1 / Production host: ![]() ![]() |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % / Description: Hexagonal rod, 0.2 x 0.05 x 0.05 mm |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 0.2 M Li2SO4, 15% (w/v) PEG 3350, 25% (v/v) glycerol Cryoprotected with 23% (w/v) PEG 3350, 25% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.39→35 Å / Num. obs: 29047 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.047 / Rrim(I) all: 0.114 / Χ2: 0.801 / Net I/σ(I): 5.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MV2 Resolution: 2.394→29.46 Å / SU ML: 0.2916 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.3856
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.394→29.46 Å
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Refine LS restraints |
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LS refinement shell |
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