+Open data
-Basic information
Entry | Database: PDB / ID: 1m2v | ||||||
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Title | Crystal Structure of the yeast Sec23/24 heterodimer | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / zinc-finger / beta barrel / vWA domain / gelsolin domain | ||||||
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 / COPII-mediated vesicle transport / COPII-coated vesicle cargo loading / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / signal sequence binding / fungal-type vacuole membrane ...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 / COPII-mediated vesicle transport / COPII-coated vesicle cargo loading / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / signal sequence binding / fungal-type vacuole membrane / reticulophagy / endoplasmic reticulum exit site / GTPase activator activity / SNARE binding / macroautophagy / intracellular protein transport / 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: 2.75 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 | 1m2v.cif.gz | 299.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m2v.ent.gz | 236.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m2v_validation.pdf.gz | 387.6 KB | Display | wwPDB validaton report |
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Full document | 1m2v_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 1m2v_validation.xml.gz | 34 KB | Display | |
Data in CIF | 1m2v_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/1m2v ftp://data.pdbj.org/pub/pdb/validation_reports/m2/1m2v | HTTPS FTP |
-Related structure data
Related structure data | 1m2oSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 85463.242 Da / Num. of mol.: 1 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 | ||
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#2: Protein | Mass: 103733.250 Da / Num. of mol.: 1 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: P40482 | ||
#3: Chemical | #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: 2.72 Å3/Da / Density % sol: 54.71 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0 M ammonium formate, 18 mM dithiothreitol, 10 % (w/v) xylitol, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP at 273K | ||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X25 / Wavelength: 1.05 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→25 Å / Num. all: 54236 / Num. obs: 49463 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 2.75→2.92 Å |
Reflection | *PLUS Num. measured all: 190671 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 63.1 % / Rmerge(I) obs: 0.252 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Sec23 from PDB ENTRY 1M2O Resolution: 2.75→19.96 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.2334 Å2 / ksol: 0.374578 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.41 Å / Luzzati sigma a free: 0.62 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor obs: 0.21 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.205 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.397 / Rfactor Rwork: 0.332 |