+Open data
-Basic information
Entry | Database: PDB / ID: 6cff | ||||||
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Title | Stimulator of Interferon Genes Human | ||||||
Components | Stimulator of interferon genes protein | ||||||
Keywords | IMMUNE SYSTEM / human STING / complex / cyclic-di-AMP / TMEM173 / wild type / 230G/232R | ||||||
Function / homology | Function and homology information STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / autophagosome assembly / cellular response to organic cyclic compound / autophagosome / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / secretory granule membrane / cytoplasmic vesicle membrane / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / protein complex oligomerization / positive regulation of protein binding / regulation of inflammatory response / defense response to virus / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / endosome / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å | ||||||
Authors | Fernandez, D. / Li, L. / Ergun, S.L. | ||||||
Citation | Journal: Cell / Year: 2019 Title: STING Polymer Structure Reveals Mechanisms for Activation, Hyperactivation, and Inhibition. Authors: Ergun, S.L. / Fernandez, D. / Weiss, T.M. / Li, L. #1: Journal: Biorxiv / Year: 2019 Title: STING polymer structure reveals mechanisms for activation, hyperactivation, and inhibition Authors: Ergun, S.L. / Fernandez, D. / Weiss, T.M. / Li, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cff.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cff.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 6cff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/6cff ftp://data.pdbj.org/pub/pdb/validation_reports/cf/6cff | HTTPS FTP |
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-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: 27123.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM173, ERIS, MITA, STING / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV6 |
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#2: Chemical | ChemComp-2BA / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.8 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: Sodium citrate tribasic, PEG 3350, pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2017 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.396→40 Å / Num. obs: 8466 / % possible obs: 97.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.048 / Rrim(I) all: 0.1 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.396→2.457 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1216 / CC1/2: 0.794 / Rpim(I) all: 0.33 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.396→20.09 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.972 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.263 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.582 Å2
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Refinement step | Cycle: 1 / Resolution: 2.396→20.09 Å
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