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Open data
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Basic information
Entry | Database: PDB / ID: 8e0c | |||||||||
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Title | Crystal structure of human Sar1bH79G | |||||||||
![]() | GTP-binding protein SAR1b | |||||||||
![]() | SIGNALING PROTEIN / Sar1b / GDP / COPII / small GTPase | |||||||||
Function / homology | ![]() lipid export from cell / amino acid sensor activity / regulation of lipid transport / regulation of COPII vesicle coating / cellular response to leucine starvation / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coating ...lipid export from cell / amino acid sensor activity / regulation of lipid transport / regulation of COPII vesicle coating / cellular response to leucine starvation / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coating / Chylomicron assembly / Regulation of cholesterol biosynthesis by SREBP (SREBF) / membrane organization / Cargo concentration in the ER / antigen processing and presentation of peptide antigen via MHC class I / COPII-mediated vesicle transport / lipoprotein transport / Golgi cisterna membrane / lipid homeostasis / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of TORC1 signaling / MHC class II antigen presentation / small monomeric GTPase / G protein activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / lysosomal membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, Q. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The alarmone ppGpp selectively inhibits the isoform A of the human small GTPase Sar1. Authors: Huang, Q. / Szebenyi, D.M.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 37.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dzmSC ![]() 8dznC ![]() 8dzoC ![]() 8dztC ![]() 8e0aC ![]() 8e0bC ![]() 8e0dC ![]() 8e0hC C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 22354.768 Da / Num. of mol.: 1 / Mutation: H79G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-GTP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2M (NH4)2SO4 and 0.1M sodium citrate, pH5.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.993→50 Å / Num. obs: 12363 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.993→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 601 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8dzm Resolution: 1.993→32.148 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.67 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.77 Å2 / Biso mean: 26.81 Å2 / Biso min: 11.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.993→32.148 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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