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- PDB-3efo: Crystal Structure of the mammalian COPII-coat protein Sec23/24 bo... -
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Open data
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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 | ||||||
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![]() | PROTEIN TRANSPORT / COPII / coat protein / transport signal / Disease mutation / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transport | ||||||
Function / homology | ![]() 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 / SNARE complex ...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 / SNARE complex / SNAP receptor activity / COPII vesicle coat / COPII vesicle coating / 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 exit site / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goldberg, J. / Mancias, J.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 306.1 KB | Display | ![]() |
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PDB format | ![]() | 249.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 457.8 KB | Display | ![]() |
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Full document | ![]() | 519.6 KB | Display | |
Data in XML | ![]() | 59.3 KB | Display | |
Data in CIF | ![]() | 80.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() | ||
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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.) ![]() ![]() ![]() | ||
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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