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- PDB-9cue: Human STING H232R variant bound to ABZI -

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Basic information

Entry
Database: PDB / ID: 9cue
TitleHuman STING H232R variant bound to ABZI
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: 1.95 Å
AuthorsSack, J.S. / Critton, 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)48,6413
Polymers48,1082
Non-polymers5341
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-17 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.104, 130.170, 35.923
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: 24053.945 Da / Num. of mol.: 2 / Fragment: residues 155-341 / Mutation: H232R 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-A1A4X / benzyl (3-{5-carbamoyl-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-methoxy-1H-1,3-benzimidazol-1-yl}propyl)carbamate


Mass: 533.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M tri-sodium citrate dihydrate pH 5.6, 20% (w/v) PEG 4,000, 20% (v/v) isopropanol

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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 PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→75.73 Å / Num. obs: 21574 / % possible obs: 91.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 1.96→2.22 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1079 / % possible all: 49.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.11.8 (20-OCT-2021)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→16.4 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.838 / SU R Cruickshank DPI: 0.756 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.317 / SU Rfree Blow DPI: 0.251 / SU Rfree Cruickshank DPI: 0.256
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1042 4.85 %RANDOM
Rwork0.307 ---
obs0.308 21504 65.3 %-
Displacement parametersBiso mean: 36.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.1294 Å20 Å20 Å2
2--0.7323 Å20 Å2
3----2.8617 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 1.95→16.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 39 23 2484
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084884HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.968760HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1420SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes787HARMONIC5
X-RAY DIFFRACTIONt_it2552HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion17.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion332SEMIHARMONIC5
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_contact3358SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.12 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4252 -6.73 %
Rwork0.3791 402 -
all0.3821 431 -
obs--5.79 %
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)
13.7041-0.26131.02220.3495-0.23411.5478-0.0106-0.06980.31950.0273-0.02720.00370.0485-0.04160.0378-0.05430.00790.0102-0.12220.0015-0.124417.1013-18.8742-0.8709
20.94710.52730.23841.7423-0.19862.56280.06790.0397-0.18550.0196-0.04430.02010.25940.0751-0.0236-0.06750.0596-0.0233-0.0527-0.0109-0.117428.386-44.73040.4183
37.4865.82085.82080-5.820800.05081.0228-0.91130.5105-1.03771.08850.9499-1.08850.987-0.12150.2343-0.1516-0.60790.304-0.420418.9154-33.2391-0.7361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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