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Yorodumi- PDB-3efo: Crystal Structure of the mammalian COPII-coat protein Sec23/24 bo... -
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-Basic information
Entry | Database: PDB / ID: 3efo | ||||||
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Title | Crystal Structure of the mammalian COPII-coat protein Sec23/24 bound to the transport signal sequence of syntaxin 5 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / COPII / coat protein / transport signal / Disease mutation / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transport | ||||||
Function / homology | Function and homology information regulation of Golgi organization / Golgi disassembly / vesicle fusion with Golgi apparatus / early endosome to Golgi transport / Intra-Golgi traffic / COPII-coated vesicle cargo loading / : / vesicle fusion / vesicle docking / COPII vesicle coat ...regulation of Golgi organization / Golgi disassembly / vesicle fusion with Golgi apparatus / early endosome to Golgi transport / Intra-Golgi traffic / COPII-coated vesicle cargo loading / : / vesicle fusion / vesicle docking / COPII vesicle coat / COPII vesicle coating / SNARE complex / SNAP receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde transport, endosome to Golgi / COPII-mediated vesicle transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / endoplasmic reticulum exit site / COPI-mediated anterograde transport / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / positive regulation of protein catabolic process / in utero embryonic development / vesicle / membrane => GO:0016020 / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / Golgi apparatus / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 3efo.cif.gz | 306.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3efo.ent.gz | 249.7 KB | Display | PDB format |
PDBx/mmJSON format | 3efo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/3efo ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3efo | 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: 86177.367 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: 86647.852 Da / Num. of mol.: 1 / Fragment: conserved core, UNP residues 267-1033 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24D / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IYI7, UniProt: O94855*PLUS | ||
#3: Protein/peptide | Mass: 793.949 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The sequence of this 7-residue synthetic peptide occurs naturally in humans References: UniProt: Q13190*PLUS | ||
#4: Chemical | #5: 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: 3.18 Å3/Da / Density % sol: 61.34 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 5.5% (w/v) PEG 4000, 0.1 M magnesium sulfate and 100 mM HEPES, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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: 2.7→50 Å / Num. obs: 58392 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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