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- PDB-9cud: Human STING G230A/R293Q variant bound to diABZI-i -

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Basic information

Entry
Database: PDB / ID: 9cud
TitleHuman STING G230A/R293Q variant bound to diABZI-i
ComponentsStimulator of interferon genes protein
KeywordsMEMBRANE PROTEIN / Innate immunity
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / proton channel activity ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / proton channel activity / cGAS/STING signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / antiviral innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / cytoplasmic vesicle membrane / Regulation of innate immune responses to cytosolic DNA / autophagosome / positive regulation of interferon-beta production / positive regulation of DNA-binding transcription factor activity / secretory granule membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / peroxisome / regulation of inflammatory response / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / ciliary basal body / cilium / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
: / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCritton, D.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Orthosteric STING inhibition elucidates molecular correction of SAVI STING
Authors: Xie, T. / Ruzanov, M. / Critton, D.A. / Merselis, L. / Naglich, J. / Sack, J.S. / Zhang, P. / Xie, C. / Tredup, J. / Stine, L.B. / Messier, C. / Caceres-Cortes, J. / Mueller, L. / Dyckman, A. ...Authors: Xie, T. / Ruzanov, M. / Critton, D.A. / Merselis, L. / Naglich, J. / Sack, J.S. / Zhang, P. / Xie, C. / Tredup, J. / Stine, L.B. / Messier, C. / Caceres-Cortes, J. / Mueller, L. / Dyckman, A.J. / Newitt, J.A. / Wilson, S.C.
History
DepositionJul 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9473
Polymers48,0782
Non-polymers8691
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-17 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.072, 122.946, 36.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Stimulator of interferon genes protein / hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / ...hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / Transmembrane protein 173


Mass: 24038.906 Da / Num. of mol.: 2 / Fragment: residues 155-341 / Mutation: G230A/R293Q variant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING1, ERIS, MITA, STING, TMEM173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV6
#2: Chemical ChemComp-A1A4W / (2E)-1-[(2E)-4-{(2E)-5-carbamoyl-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)imino]-3-methyl-2,3-dihydro-1H-1,3-benzimidazol-1-yl}-2,3-dimethylbut-2-en-1-yl]-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)imino]-7-[(3-methoxyphenyl)methoxy]-3-methyl-2,3-dihydro-1H-1,3-benzimidazole-5-carboxamide


Mass: 868.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H52N12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.87 Å3/Da / Density % sol: 34.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris pH 5.5, 0.2 M magnesium chloride, 25% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→67.1 Å / Num. obs: 40347 / % possible obs: 80.6 % / Redundancy: 4.1 % / CC1/2: 0.999 / Net I/σ(I): 12.4
Reflection shellResolution: 1.52→1.63 Å / Redundancy: 3.34 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1739 / CC1/2: 0.564 / % possible all: 44.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.11.8 (16-JUL-2021)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→21.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.118
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2043 5.07 %RANDOM
Rwork0.226 ---
obs0.227 40328 72.3 %-
Displacement parametersBiso mean: 21.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.1332 Å20 Å20 Å2
2---0.8856 Å20 Å2
3---0.7524 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.53→21.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 64 309 2828
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085197HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.919333HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1544SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes825HARMONIC5
X-RAY DIFFRACTIONt_it2678HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion15.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion333SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4308SEMIHARMONIC4
LS refinement shellResolution: 1.53→1.6 Å
RfactorNum. reflection% reflection
Rfree0.34 -4.34 %
Rwork0.2658 772 -
obs--10.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.48940.4991-0.08971.6577-0.04970.3760.0331-0.1964-0.03180.0455-0.0402-0.33560.04120.02130.0071-0.1637-0.0106-0.0118-0.1654-0.007-0.1193-7.311520.5932-17.0539
20.64840.0097-0.17610.7601-0.16860.55060.0114-0.0122-0.1169-0.1046-0.0388-0.0389-0.01080.03260.0274-0.1614-0.0011-0.0016-0.1579-0.0044-0.1434-26.4215-2.5445-18.5179
301.78420.17042.10812.0682.21320.0007-0.1534-0.14380.0511-0.0123-0.09290.02540.06380.01150.0171-0.01490.00420.00490.00640.0512-13.88426.49-18.086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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