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Yorodumi- PDB-1pcx: Crystal structure of the COPII coat subunit, Sec24, complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pcx | ||||||
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Title | Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide from the SNARE protein Bet1 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information : / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / Intra-Golgi traffic / positive regulation of ER to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / COPII-mediated vesicle transport / COPII-coated vesicle cargo loading / vesicle fusion / COPII vesicle coat ...: / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / Intra-Golgi traffic / positive regulation of ER to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / COPII-mediated vesicle transport / COPII-coated vesicle cargo loading / vesicle fusion / COPII vesicle coat / SNARE complex / SNAP receptor activity / positive regulation of protein exit from endoplasmic reticulum / signal sequence binding / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / fungal-type vacuole membrane / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / SNARE binding / macroautophagy / intracellular protein transport / protein transport / membrane => GO:0016020 / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mossessova, E. / Bickford, L.C. / Goldberg, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: SNARE selectivity of the COPII coat. Authors: Mossessova, E. / Bickford, L.C. / Goldberg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pcx.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pcx.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/1pcx ftp://data.pdbj.org/pub/pdb/validation_reports/pc/1pcx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 90841.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sec24 fragment lacking n-terminal residues 1-116 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40482 |
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#2: Protein/peptide | Mass: 833.885 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE References: UniProt: P22804 |
#3: Chemical | ChemComp-ZN / |
#4: 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: 2.82 Å3/Da / Density % sol: 56.34 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: sodium acetate 1,6-hexanediol, cobalt chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 34136 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.0999 / Net I/σ(I): 47.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3076 / Rsym value: 0.0999 / % possible all: 86.3 |
Reflection | *PLUS Num. measured all: 294648 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 86.3 % / Num. unique obs: 3076 / Num. measured obs: 19905 / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.78 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.1311 Å2 / ksol: 0.291041 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.216 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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