[English] 日本語
Yorodumi- PDB-6wc3: Crystal structure of the SNARE Sec20 bound to Dsl1 complex subuni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wc3 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the SNARE Sec20 bound to Dsl1 complex subunit Tip20 | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSPORT PROTEIN / membrane trafficking / SNARE protein / COPI / vesicle / multisubunit tethering complex / Dsl1 complex / CATCHR complex | ||||||||||||
Function / homology | Function and homology information Dsl1/NZR complex / regulation of ER to Golgi vesicle-mediated transport / SNARE complex / SNAP receptor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / autophagy / membrane => GO:0016020 / endoplasmic reticulum Similarity search - Function | ||||||||||||
Biological species | Ashbya gossypii (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.203 Å | ||||||||||||
Authors | Travis, S.M. / Jeffrey, P.D. / Hughson, F.M. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structural basis for the binding of SNAREs to the multisubunit tethering complex Dsl1. Authors: Travis, S.M. / DAmico, K. / Yu, I.M. / McMahon, C. / Hamid, S. / Ramirez-Arellano, G. / Jeffrey, P.D. / Hughson, F.M. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6wc3.cif.gz | 150 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6wc3.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/6wc3 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/6wc3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3fhnS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 68547.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus) Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_ADL286W / Plasmid: pQLinkH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q75B58 |
---|---|
#2: Protein | Mass: 15632.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus) Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_AFR344C / Plasmid: pQLinkN / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q753G8 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 72 % / Description: rounded hexagonal, 100 x 100 x 100 um |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M sodium citrate, pH 6.0, 0.725 M ammonium sulfate, 1 mM dithiothreitol, cryoprotected with 30% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 20, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→29.26 Å / Num. obs: 25597 / % possible obs: 99 % / Redundancy: 26 % / Biso Wilson estimate: 85.28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.026 / Rrim(I) all: 0.135 / Net I/σ(I): 27.6 / Num. measured all: 666066 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FHN Resolution: 3.203→28.294 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.14 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 215.6 Å2 / Biso mean: 79.4855 Å2 / Biso min: 33.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.203→28.294 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|