+Open data
-Basic information
Entry | Database: PDB / ID: 5kyw | ||||||
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Title | crystal structure of Sec23 and TANGO1 peptide3 complex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / COPII coat / collagen secretion / cargo adapter / vesicle | ||||||
Function / homology | Function and homology information vesicle cargo loading / negative regulation of lymphocyte migration / protein localization to endoplasmic reticulum exit site / cellular response to oxidised low-density lipoprotein particle stimulus / COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / negative regulation of leukocyte cell-cell adhesion / negative regulation of cell adhesion ...vesicle cargo loading / negative regulation of lymphocyte migration / protein localization to endoplasmic reticulum exit site / cellular response to oxidised low-density lipoprotein particle stimulus / COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / negative regulation of leukocyte cell-cell adhesion / negative regulation of cell adhesion / endoplasmic reticulum organization / cell migration involved in sprouting angiogenesis / cargo receptor activity / COPII-mediated vesicle transport / positive regulation of leukocyte migration / lipoprotein transport / exocytosis / endoplasmic reticulum exit site / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class II antigen presentation / negative regulation of cell migration / GTPase activator activity / SNARE binding / protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Post-translational protein phosphorylation / intracellular protein transport / wound healing / ER to Golgi transport vesicle membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / protein transport / in utero embryonic development / endoplasmic reticulum lumen / Golgi membrane / intracellular membrane-bounded organelle / 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 / Resolution: 3.2 Å | ||||||
Authors | Ma, W. / Goldberg, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: TANGO1/cTAGE5 receptor as a polyvalent template for assembly of large COPII coats. Authors: Ma, W. / Goldberg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kyw.cif.gz | 606.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kyw.ent.gz | 512.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kyw_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 5kyw_full_validation.pdf.gz | 465.4 KB | Display | |
Data in XML | 5kyw_validation.xml.gz | 51.6 KB | Display | |
Data in CIF | 5kyw_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/5kyw ftp://data.pdbj.org/pub/pdb/validation_reports/ky/5kyw | HTTPS FTP |
-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: 86249.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q15436 | ||
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#2: Protein | Mass: 86647.852 Da / Num. of mol.: 1 / Fragment: unp residues 266-1032 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24D, KIAA0755 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O94855 | ||
#3: Protein/peptide | Mass: 912.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JRA6*PLUS | ||
#4: Chemical | Sequence details | TANGO1 peptide3 LPPPFGPGM is derived from human TANGO1 protein (1800-1808) | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 5.5 % (w/v) PEG 4000, 100 mM MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→82.512 Å / Num. obs: 36535 / % possible obs: 99.9 % / Redundancy: 3.2 % / Net I/σ(I): 10.6 |
-Processing
Software |
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Refinement | Resolution: 3.2→82.512 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→82.512 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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