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- PDB-7kvz: Structure of hSTING in complex with novel carbocyclic pyrimidine CDN-2 -

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Basic information

Entry
Database: PDB / ID: 7kvz
TitleStructure of hSTING in complex with novel carbocyclic pyrimidine CDN-2
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE 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 / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle ...2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm
Similarity search - Function
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173
Similarity search - Domain/homology
Chem-X5D / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSkene, R.J.
CitationJournal: 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
DepositionNov 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers27,2121
Non-polymers6171
Water1,08160
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6584
Polymers54,4232
Non-polymers1,2352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4300 Å2
ΔGint-17 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.441, 78.273, 35.934
Angle α, β, γ (deg.)90.000, 96.790, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Stimulator of interferon genes protein / Transmembrane protein 173


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-X5D / (2R,5R,7R,8R,10S,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2,10,16-trihydroxy-14-[(pyrimidin-4-yl)oxy]decahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione


Mass: 617.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20.0% PEG 3350, 0.2M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.35→44.45 Å / Num. obs: 9973 / % possible obs: 96.6 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.047 / Rrim(I) all: 0.086 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.433.50.56334729930.7260.3530.6661.699.7
9.1-44.413.20.0395841850.9970.0250.04723.597.7

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KSY

4ksy


Resolution: 2.35→44.446 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.938 / SU B: 16.783 / SU ML: 0.172 / SU R Cruickshank DPI: 0.2948 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 466 4.7 %RANDOM
Rwork0.1752 ---
obs0.1777 9507 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.41 Å2 / Biso mean: 59.663 Å2 / Biso min: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å21.78 Å2
2--1.63 Å20 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 2.35→44.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 41 60 1566
Biso mean--32.67 57.66 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121542
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.6842097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79121.56296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7215255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3491515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021231
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 39 -
Rwork0.278 722 -
all-761 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: 29.789 Å / Origin y: 7.958 Å / Origin z: 17.327 Å
111213212223313233
T0.0516 Å2-0.0141 Å2-0.0742 Å2-0.0479 Å2-0.0085 Å2--0.1464 Å2
L0.831 °2-0.5547 °20.1217 °2-1.6251 °20.1678 °2--0.7762 °2
S-0.0624 Å °-0.0363 Å °0.1683 Å °-0.0553 Å °0.0588 Å °0.1464 Å °0.1006 Å °-0.1518 Å °0.0037 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A152 - 336
2X-RAY DIFFRACTION1A2500
3X-RAY DIFFRACTION1A2601 - 2660

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