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- PDB-4ef5: Crystal structure of STING CTD -

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Basic information

Entry
Database: PDB / ID: 4ef5
TitleCrystal structure of STING CTD
ComponentsTransmembrane protein 173
KeywordsIMMUNE SYSTEM / STING/MITA/ERIS/MPYS/TMEM173 / innate immune system / type I interferon / dimerization / c-di-GMP / 5 helices and 5 strands in single domain
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsOuyang, S. / Ru, H. / Shaw, N. / Jiang, Y. / Niu, F. / Zhu, Y. / Qiu, W. / Li, Y. / Liu, Z.-J.
CitationJournal: Immunity / Year: 2012
Title: Structural analysis of the STING adaptor protein reveals a hydrophobic dimer interface and mode of cyclic di-GMP binding
Authors: Ouyang, S. / Song, X. / Wang, Y. / Ru, H. / Shaw, N. / Jiang, Y. / Niu, F. / Zhu, Y. / Qiu, W. / Parvatiyar, K. / Li, Y. / Zhang, R. / Cheng, G. / Liu, Z.J.
History
DepositionMar 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2May 30, 2012Group: Database references
Revision 1.3Jul 3, 2013Group: Database references
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protein 173


Theoretical massNumber of molelcules
Total (without water)29,8481
Polymers29,8481
Non-polymers00
Water37821
1
A: Transmembrane protein 173

A: Transmembrane protein 173


Theoretical massNumber of molelcules
Total (without water)59,6972
Polymers59,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1880 Å2
ΔGint-15 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.041, 90.356, 73.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

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


Mass: 29848.463 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING/MITA/ERIS/MPYS/TMEM173 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86WV6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14.4%(w/v) PEG8000, 0.08M Cacodylate, 0.16M calcium acetate, 20%(v/v) glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→45.18 Å / Num. all: 10182 / Num. obs: 10182 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.45 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→45.178 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8033 / SU ML: 0.37 / Cross valid method: THROUGHOUT / Phase error: 25.89 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2879 488 4.79 %RANDOM
Rwork0.2265 ---
obs0.2293 10182 99.85 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.567 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 127.43 Å2 / Biso mean: 64.6145 Å2 / Biso min: 28.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.145 Å20 Å2-0 Å2
2--0.9679 Å20 Å2
3----0.8228 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 0 21 1454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061485
X-RAY DIFFRACTIONf_angle_d1.0032015
X-RAY DIFFRACTIONf_chiral_restr0.067221
X-RAY DIFFRACTIONf_plane_restr0.004266
X-RAY DIFFRACTIONf_dihedral_angle_d16.417567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4501-2.80460.29731660.267131553321
2.8046-3.53330.31221660.204132113377
3.5333-45.18570.27611560.228133283484

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