+Open data
-Basic information
Entry | Database: PDB / ID: 1m2o | ||||||
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Title | Crystal Structure of the Sec23-Sar1 complex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/SIGNALING PROTEIN / zinc-finger / beta barrel / vWA domain / gelsolin domain / PROTEIN TRANSPORT-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat ...Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / mitochondrial fission / mitochondrial membrane organization / reticulophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / GTPase activator activity / macroautophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / zinc ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Bi, X. / Corpina, R.A. / Goldberg, J. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Structure of the Sec23/24-Sar1 pre-budding complex of the COPII vesicle coat Authors: Bi, X. / Corpina, R.A. / Goldberg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m2o.cif.gz | 360.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m2o.ent.gz | 287.2 KB | Display | PDB format |
PDBx/mmJSON format | 1m2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/1m2o ftp://data.pdbj.org/pub/pdb/validation_reports/m2/1m2o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 85463.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Sec23 / Production host: Escherichia coli (E. coli) / References: UniProt: P15303 #2: Protein | Mass: 21472.564 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Sar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20606 |
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-Non-polymers , 4 types, 177 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.67 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 270 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% (w/v) PEG 1500, 10% (w/v) isopropanol, 0.2 M ammonium acetate, 50 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 270K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||||||||
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: CHESS / Beamline: F2 / Wavelength: 1 Å |
Detector | Type: KODAK / Detector: IMAGE PLATE / Date: Nov 5, 2001 |
Radiation | Monochromator: CHESS F-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 68753 / Num. obs: 63872 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 2.5→2.66 Å |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 289977 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 79.9 % / Rmerge(I) obs: 0.237 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→23.85 Å / Rfactor Rfree error: 0.005 / 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 | Solvent model: FLAT MODEL / Bsol: 23.6345 Å2 / ksol: 0.312224 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.45 Å / Luzzati sigma a free: 0.42 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→23.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor all: 0.238 / Rfactor obs: 0.238 / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.238 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.368 / Rfactor Rwork: 0.282 |