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Yorodumi- PDB-3egx: Crystal structure of the mammalian COPII-coat protein Sec23a/24a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3egx | ||||||
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Title | Crystal structure of the mammalian COPII-coat protein Sec23a/24a complexed with the SNARE protein Sec22b and bound to the transport signal sequence of the SNARE protein Bet1 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / COPII coat protein / vesicle transport / transport signal sequence / Disease mutation / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transport / Phosphoprotein / Transmembrane | ||||||
Function / homology | Function and homology information : / vesicle fusion with Golgi apparatus / Golgi trans cisterna / regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPII vesicle coat / COPII vesicle coating / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity ...: / vesicle fusion with Golgi apparatus / Golgi trans cisterna / regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPII vesicle coat / COPII vesicle coating / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / COPI-mediated anterograde transport / transport vesicle / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / cholesterol homeostasis / protein localization to plasma membrane / positive regulation of protein secretion / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / phagocytic vesicle membrane / positive regulation of protein catabolic process / melanosome / protein transport / ER-Phagosome pathway / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / zinc ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å | ||||||
Authors | Goldberg, J. / Mancias, J.D. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Structural basis of cargo membrane protein discrimination by the human COPII coat machinery. Authors: Mancias, J.D. / Goldberg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3egx.cif.gz | 327.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3egx.ent.gz | 258.1 KB | Display | PDB format |
PDBx/mmJSON format | 3egx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/3egx ftp://data.pdbj.org/pub/pdb/validation_reports/eg/3egx | 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: 86178.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15436 |
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#2: Protein | Mass: 84336.820 Da / Num. of mol.: 1 / Fragment: Conserved core, UNP residues 346-1093 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95486 |
#3: Protein | Mass: 18031.645 Da / Num. of mol.: 1 / Fragment: cytoplasmic domainn, UNP residues 1-157 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEC22B, SEC22L1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75396 |
#4: Protein/peptide | Mass: 1000.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic 9-residue peptide / References: UniProt: O15155*PLUS |
#5: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 10% (w/v) PEG 4000, 0.1 M NaCl, 0.5 M sodium acetate, 50 mM Tris buffer, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→25 Å / Num. obs: 24079 / % possible obs: 92 % / Observed criterion σ(F): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.2 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.3→25 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.3→25 Å
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