[English] 日本語
Yorodumi- PDB-7kvx: Structure of hSTING in complex with novel carbocyclic pyrimidine CDN 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kvx | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of hSTING in complex with novel carbocyclic pyrimidine CDN 1 | ||||||
Components | Stimulator of interferon genes protein | ||||||
Keywords | IMMUNE SYSTEM / immunotherapy / stimulator of interferon genes / cyclic dinucleotide | ||||||
Function / homology | Function and homology information 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / positive regulation of type I interferon production / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / monoatomic ion transmembrane transport ...2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / positive regulation of type I interferon production / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / monoatomic ion transmembrane transport / 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 / Resolution: 2.48 Å | ||||||
Authors | Skene, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Identification of Novel Carbocyclic Pyrimidine Cyclic Dinucleotide STING Agonists for Antitumor Immunotherapy Using Systemic Intravenous Route. Authors: Vyskocil, S. / Cardin, D. / Ciavarri, J. / Conlon, J. / Cullis, C. / England, D. / Gershman, R. / Gigstad, K. / Gipson, K. / Gould, A. / Greenspan, P. / Griffin, R. / Gulavita, N. / ...Authors: Vyskocil, S. / Cardin, D. / Ciavarri, J. / Conlon, J. / Cullis, C. / England, D. / Gershman, R. / Gigstad, K. / Gipson, K. / Gould, A. / Greenspan, P. / Griffin, R. / Gulavita, N. / Harrison, S. / Hu, Z. / Hu, Y. / Hata, A. / Huang, J. / Huang, S.C. / Janowick, D. / Jones, M. / Kolev, V. / Langston, S.P. / Lee, H.M. / Li, G. / Lok, D. / Ma, L. / Mai, D. / Malley, J. / Matsuda, A. / Mizutani, H. / Mizutani, M. / Molchanova, N. / Nunes, E. / Pusalkar, S. / Renou, C. / Rowland, S. / Sato, Y. / Shaw, M. / Shen, L. / Shi, Z. / Skene, R. / Soucy, F. / Stroud, S. / Xu, H. / Xu, T. / Abu-Yousif, A.O. / Zhang, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7kvx.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7kvx.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 7kvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kvx_validation.pdf.gz | 897.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7kvx_full_validation.pdf.gz | 898.6 KB | Display | |
Data in XML | 7kvx_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7kvx_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/7kvx ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kvx | HTTPS FTP |
-Related structure data
Related structure data | 7kvzC 7kw1C 4ksyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27211.619 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 (E. coli) / References: UniProt: A0A2R3XZB7 |
---|---|
#2: Chemical | ChemComp-X5J / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 26.0% PEG 3350, 0.200M Ammonium Sulfate, 0.1M bis-tris pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.1806 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1806 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.48→44.46 Å / Num. obs: 8802 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.057 / Rrim(I) all: 0.119 / Net I/σ(I): 8.4 / Num. measured all: 36429 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KSY Resolution: 2.48→35.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 23.755 / SU ML: 0.245 / SU R Cruickshank DPI: 0.3882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.65 Å2 / Biso mean: 60.133 Å2 / Biso min: 32.21 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.48→35.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.48→2.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 29.7099 Å / Origin y: 7.8942 Å / Origin z: 17.3516 Å
|