+Open data
-Basic information
Entry | Database: PDB / ID: 8e0c | |||||||||
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Title | Crystal structure of human Sar1bH79G | |||||||||
Components | GTP-binding protein SAR1b | |||||||||
Keywords | SIGNALING PROTEIN / Sar1b / GDP / COPII / small GTPase | |||||||||
Function / homology | Function and homology information regulation of lipid transport / regulation of COPII vesicle coating / Chylomicron assembly / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / antigen processing and presentation of peptide antigen via MHC class I ...regulation of lipid transport / regulation of COPII vesicle coating / Chylomicron assembly / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / Regulation of cholesterol biosynthesis by SREBP (SREBF) / 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 to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.993 Å | |||||||||
Authors | Huang, Q. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proteins / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e0c.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e0c.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 8e0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/8e0c ftp://data.pdbj.org/pub/pdb/validation_reports/e0/8e0c | HTTPS FTP |
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-Related structure data
Related structure data | 8dzmSC 8dznC 8dzoC 8dztC 8e0aC 8e0bC 8e0dC 8e0hC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Homo sapiens (human) / Gene: SAR1B, SARA2, SARB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6B6 | ||||
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#2: Chemical | ChemComp-GTP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9778 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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