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Yorodumi- PDB-6ukz: STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Co... -
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-Basic information
Entry | Database: PDB / ID: 6ukz | ||||||
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Title | STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 6 | ||||||
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) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / autophagosome membrane / protein sumoylation / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / condensed nuclear chromosome / protein tag activity / cytoplasmic vesicle / mitochondrial outer membrane / nucleotide binding / 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 / MOLECULAR REPLACEMENT / Resolution: 1.52 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 | 6ukz.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ukz.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ukz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/6ukz ftp://data.pdbj.org/pub/pdb/validation_reports/uk/6ukz | HTTPS FTP |
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-Related structure data
Related structure data | 6ukmSC 6ukuC 6ukvC 6ukwC 6ukxC 6ukyC 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
#1: Protein | Mass: 34456.527 Da / Num. of mol.: 2 / 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 #2: Chemical | ChemComp-QBG / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 22.46 % / Mosaicity: 0.08 ° |
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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: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→36.278 Å / Num. obs: 67964 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.017 / Rrim(I) all: 0.031 / Rsym value: 0.027 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.522→1.548 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.1 / Num. measured all: 35570 / Num. unique obs: 10157 / CC1/2: 0.853 / Rpim(I) all: 0.254 / Rrim(I) all: 0.481 / Rsym value: 0.493 / Net I/σ(I) obs: 2.5 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 6UKM Resolution: 1.52→22.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.072
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Displacement parameters | Biso max: 123.73 Å2 / Biso mean: 31.97 Å2 / Biso min: 12.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.52→22.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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