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Yorodumi- PDB-1mqs: Crystal structure of Sly1p in complex with an N-terminal peptide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mqs | ||||||
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Title | Crystal structure of Sly1p in complex with an N-terminal peptide of Sed5p | ||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / SM-protein / SNARE / syntaxin / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information regulation of inclusion body assembly / Cargo concentration in the ER / Golgi cis cisterna membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / regulation of Ras protein signal transduction / COPI-mediated anterograde transport / COPII-mediated vesicle transport / vesicle fusion ...regulation of inclusion body assembly / Cargo concentration in the ER / Golgi cis cisterna membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / regulation of Ras protein signal transduction / COPI-mediated anterograde transport / COPII-mediated vesicle transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / vesicle docking involved in exocytosis / positive regulation of SNARE complex assembly / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / syntaxin binding / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / vesicle-mediated transport / SNARE binding / intracellular protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Bracher, A. / Weissenhorn, W. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Structural basis for the Golgi membrane recruitment of Sly1p by Sed5p Authors: Bracher, A. / Weissenhorn, W. #1: Journal: Nature / Year: 2000 Title: Three-dimensional structure of the neuronal-Sec1-syntaxin 1a complex Authors: Misura, K.M.S. / Scheller, R.H. / Weis, W.I. #2: Journal: Structure / Year: 2000 Title: The X-ray crystal structure of neuronal Sec1 from squid sheds new light on the role of this protein in exocytosis Authors: Bracher, A. / Perrakis, A. / Dresbach, T. / Betz, H. / Weissenhorn, W. #3: Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structures of neuronal squid Sec1 implicate inter-domain hinge movement in the release of t-SNAREs Authors: Bracher, A. / Weissenhorn, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mqs.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqs.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqs ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqs | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 75655.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PMAL-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 codon+ / References: UniProt: P22213 |
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#2: Protein/peptide | Mass: 5949.565 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 codon+ / References: UniProt: Q01590 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.89 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 3.5M sodium formate, 20mM Tris HCl pH 7.2, 50mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9875,0.9793,0.9789,0.9184 | |||||||||||||||
Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→30 Å / Num. all: 26182 / Num. obs: 26182 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 92.3 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.3 | |||||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.552 / % possible all: 100 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 200527 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→30 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 52.0133 Å2 / ksol: 0.31282 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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