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Yorodumi- PDB-6uky: STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uky | ||||||
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Title | STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 12 | ||||||
Components | fusion protein of Ubiquitin-like protein SMT3 and Stimulator of interferon protein c-terminal domain | ||||||
Keywords | IMMUNE SYSTEM / AGONIST / STING (STIMULATOR OF INTERFERON GENES) / TRANSMEMBRANE PROTEIN 173 (TMEM173) / IMMUNE SYSTEM-INHIBITOR COMPLEX / IMMUNE SYSTEM-AGONIST COMPLEX | ||||||
Function / homology | Function and homology information SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / 2',3'-cyclic GMP-AMP binding / SUMOylation of SUMOylation proteins / cyclic-di-GMP binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / reticulophagy / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / autophagosome membrane / positive regulation of macroautophagy / protein sumoylation / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / condensed nuclear chromosome / PML body / protein tag activity / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Lesburg, C.A. | ||||||
Citation | Journal: Science / Year: 2020 Title: An orally available non-nucleotide STING agonist with antitumor activity. Authors: Pan, B.S. / Perera, S.A. / Piesvaux, J.A. / Presland, J.P. / Schroeder, G.K. / Cumming, J.N. / Trotter, B.W. / Altman, M.D. / Buevich, A.V. / Cash, B. / Cemerski, S. / Chang, W. / Chen, Y. / ...Authors: Pan, B.S. / Perera, S.A. / Piesvaux, J.A. / Presland, J.P. / Schroeder, G.K. / Cumming, J.N. / Trotter, B.W. / Altman, M.D. / Buevich, A.V. / Cash, B. / Cemerski, S. / Chang, W. / Chen, Y. / Dandliker, P.J. / Feng, G. / Haidle, A. / Henderson, T. / Jewell, J. / Kariv, I. / Knemeyer, I. / Kopinja, J. / Lacey, B.M. / Laskey, J. / Lesburg, C.A. / Liang, R. / Long, B.J. / Lu, M. / Ma, Y. / Minnihan, E.C. / O'Donnell, G. / Otte, R. / Price, L. / Rakhilina, L. / Sauvagnat, B. / Sharma, S. / Tyagarajan, S. / Woo, H. / Wyss, D.F. / Xu, S. / Bennett, D.J. / Addona, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uky.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uky.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 6uky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uky_validation.pdf.gz | 321.2 KB | Display | wwPDB validaton report |
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Full document | 6uky_full_validation.pdf.gz | 321.4 KB | Display | |
Data in XML | 6uky_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6uky_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/6uky ftp://data.pdbj.org/pub/pdb/validation_reports/uk/6uky | HTTPS FTP |
-Related structure data
Related structure data | 6ukmSC 6ukuC 6ukvC 6ukwC 6ukxC 6ukzC 6ul0C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34456.527 Da / Num. of mol.: 1 / Mutation: G230A,R293Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Homo sapiens (human) Strain: ATCC 204508 / S288c Gene: SMT3, YDR510W, D9719.15, STING, LOC340061, hCG_1782396 Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)) / References: UniProt: Q12306, UniProt: A0A2R3XZB7 |
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#2: Chemical | ChemComp-QBD / |
#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: 1.6 Å3/Da / Density % sol: 22.9 % / Mosaicity: 0.19 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→55.39 Å / Num. obs: 16545 / % possible obs: 98.1 % / Redundancy: 12.7 % / Biso Wilson estimate: 33.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.037 / Rrim(I) all: 0.132 / Rsym value: 0.126 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.95→1.956 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.348 / Mean I/σ(I) obs: 2 / Num. measured all: 31524 / Num. unique obs: 2404 / CC1/2: 0.831 / Rpim(I) all: 0.299 / Rrim(I) all: 1.09 / Rsym value: 1.348 / Net I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdbid 6UKM Resolution: 1.95→55.39 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.144 / SU Rfree Cruickshank DPI: 0.137
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Displacement parameters | Biso max: 123.83 Å2 / Biso mean: 37.92 Å2 / Biso min: 15.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→55.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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