[English] 日本語
![](img/lk-miru.gif)
- PDB-6ul0: STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Co... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ul0 | ||||||
---|---|---|---|---|---|---|---|
Title | STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 4 | ||||||
![]() | fusion protein of Ubiquitin-like protein SMT3 and Stimulator of interferon protein c-terminal domain | ||||||
![]() | IMMUNE SYSTEM / AGONIST / STING (STIMULATOR OF INTERFERON GENES) / TRANSMEMBRANE PROTEIN 173 (TMEM173) / IMMUNE SYSTEM-INHIBITOR COMPLEX / IMMUNE SYSTEM-AGONIST COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lesburg, C.A. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 94.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 344 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 345.1 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 4.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ukmC ![]() 6ukuC ![]() 6ukvC ![]() 6ukwC ![]() 6ukxC ![]() 6ukyC ![]() 6ukzC ![]() 4ksyS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c Gene: SMT3, YDR510W, D9719.15, STING, LOC340061, hCG_1782396 Plasmid: pET47b / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-QBJ / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.54 Å3/Da / Density % sol: 20.29 % / Mosaicity: 0.15 ° |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→47.61 Å / Num. obs: 16734 / % possible obs: 80.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.032 / Rrim(I) all: 0.06 / Rsym value: 0.055 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.762→1.891 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1 / Num. measured all: 6920 / Num. unique obs: 1995 / CC1/2: 0.893 / Rpim(I) all: 0.262 / Rrim(I) all: 0.496 / Rsym value: 0.743 / Net I/σ(I) obs: 2.8 / % possible all: 21.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdbid 4KSY Resolution: 1.76→47.61 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.139
| ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.14 Å2 / Biso mean: 38.33 Å2 / Biso min: 3.53 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.76→47.61 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.76→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 31.8045 Å / Origin y: 0.0184 Å / Origin z: 15.8957 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|* } |