+Open data
-Basic information
Entry | Database: PDB / ID: 6ydb | ||||||
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Title | Human wtSTING in complex with 2',2'-difluoro-3',3'-c-di-GMP | ||||||
Components | Stimulator of interferon protein | ||||||
Keywords | PROTEIN BINDING / innate immune system / cyclic dinucleotide / STING | ||||||
Function / homology | Function and homology information 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle ...2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.801 Å | ||||||
Authors | Boura, E. / Smola, M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein. Authors: Smola, M. / Gutten, O. / Dejmek, M. / Kozisek, M. / Evangelidis, T. / Tehrani, Z.A. / Novotna, B. / Nencka, R. / Birkus, G. / Rulisek, L. / Boura, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ydb.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydb.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 6ydb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ydb_validation.pdf.gz | 794.7 KB | Display | wwPDB validaton report |
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Full document | 6ydb_full_validation.pdf.gz | 795.5 KB | Display | |
Data in XML | 6ydb_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 6ydb_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydb ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydb | HTTPS FTP |
-Related structure data
Related structure data | 6y99C 6ydzC 6yeaC 6z0zC 6z15C 4ksyS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 23189.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R3XZB7 |
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#2: Chemical | ChemComp-GGF / |
#3: 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: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium chloride, 0.1 M Na/K phosphate pH 6.2, 40% (v/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.801→39.275 Å / Num. obs: 5861 / % possible obs: 99.07 % / Redundancy: 15.7 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 9.71 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 561 / CC1/2: 0.581 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KSY Resolution: 2.801→39.2741 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 129.11 Å2 / Biso mean: 65.9723 Å2 / Biso min: 36.86 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.801→39.2741 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %
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