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- PDB-4emt: Crystal Structure of human STING bound to c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 4emt
TitleCrystal Structure of human STING bound to c-di-GMP
ComponentsTransmembrane protein 173
KeywordsMEMBRANE PROTEIN / alpha/beta fold / innate immune sensor / c-di-GMP / c-di-AMP
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 / positive regulation of lysosome organization / STING mediated induction of host immune responses / positive regulation of type I interferon-mediated signaling pathway / antibacterial innate immune response / IRF3-mediated induction of type I IFN ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of lysosome organization / STING mediated induction of host immune responses / positive regulation of type I interferon-mediated signaling pathway / antibacterial innate immune response / IRF3-mediated induction of type I IFN / proton channel activity / serine/threonine protein kinase complex / endolysosome membrane / reticulophagy / phosphatidylinositol-3,5-bisphosphate binding / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / negative regulation of glycolytic process / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / cholesterol binding / positive regulation of macroautophagy / lipid homeostasis / protein complex oligomerization / autophagosome membrane / autophagosome assembly / Dengue virus activates/modulates innate and adaptive immune responses / positive regulation of defense response to virus by host / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / signaling adaptor activity / positive regulation of interferon-beta production / negative regulation of TORC1 signaling / autophagosome / secretory granule membrane / Regulation of innate immune responses to cytosolic DNA / cytoplasmic vesicle membrane / positive regulation of cytokine production / protein serine/threonine kinase binding / trans-Golgi network membrane / antiviral innate immune response / autophagy / cellular senescence / SARS-CoV-1 activates/modulates innate immune responses / peroxisome / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / transcription coactivator activity / endosome / innate immune response / Golgi membrane / ubiquitin protein ligase binding / Neutrophil degranulation / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / 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
Chem-C2E / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsLi, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of STING bound to cyclic di-GMP reveals the mechanism of cyclic dinucleotide recognition by the immune system.
Authors: Shu, C. / Yi, G. / Watts, T. / Kao, C.C. / Li, P.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane protein 173
B: Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9664
Polymers43,2362
Non-polymers7302
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-19 kcal/mol
Surface area18060 Å2
MethodPISA
2
A: Transmembrane protein 173
B: Transmembrane protein 173
hetero molecules

A: Transmembrane protein 173
B: Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9338
Polymers86,4724
Non-polymers1,4614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area6510 Å2
ΔGint-53 kcal/mol
Surface area34980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.797, 78.215, 128.222
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
11B-631-

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: 21617.947 Da / Num. of mol.: 2 / Fragment: UNP residues 155 - 341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM173, ERIS, MITA, STING / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV6
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG400, 0.2M CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9839 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2012
RadiationMonochromator: Si Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9839 Å / Relative weight: 1
ReflectionResolution: 1.5→48.3 Å / Num. all: 54857 / Num. obs: 54857 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.53 Å / % possible all: 78.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX1.7_650model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→48.25 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2000 3.65 %
Rwork0.188 --
obs0.188 54811 97.1 %
all-54829 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.62 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.806 Å2-0 Å2-0 Å2
2---4.245 Å20 Å2
3----8.561 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 47 278 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062937
X-RAY DIFFRACTIONf_angle_d1.0813994
X-RAY DIFFRACTIONf_dihedral_angle_d15.0391102
X-RAY DIFFRACTIONf_chiral_restr0.076437
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53740.3271160.30593050X-RAY DIFFRACTION79
1.5374-1.5790.31641270.28513373X-RAY DIFFRACTION88
1.579-1.62540.30041400.25183704X-RAY DIFFRACTION96
1.6254-1.67790.25611440.22423794X-RAY DIFFRACTION99
1.6779-1.73790.22351470.21043864X-RAY DIFFRACTION100
1.7379-1.80740.23371460.1943853X-RAY DIFFRACTION100
1.8074-1.88970.19721440.18953825X-RAY DIFFRACTION100
1.8897-1.98930.20911460.18863846X-RAY DIFFRACTION100
1.9893-2.1140.20751480.18163901X-RAY DIFFRACTION100
2.114-2.27720.17461460.17723867X-RAY DIFFRACTION100
2.2772-2.50630.2081470.18073884X-RAY DIFFRACTION100
2.5063-2.8690.21751470.19063896X-RAY DIFFRACTION100
2.869-3.61440.19611480.17613911X-RAY DIFFRACTION99
3.6144-48.27410.20621540.1794043X-RAY DIFFRACTION99
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)
1-0.00480.5550.37391.13690.03011.2332-0.04470.0124-0.0671-0.18510.0983-0.04930.06190.26560.00390.210.0423-0.00770.26740.01270.189855.71720.212260.8383
20.33330.36910.01670.32080.00550.37620.0389-0.0595-0.10080.17430.08740.0460.0857-0.2022-0.00020.32970.0087-0.02880.28590.01350.22148.005217.572455.1236
30.47620.03141.17180.4464-0.92322.19160.01230.0305-0.06750.0970.02220.0184-0.26180.08480.00020.21630.0056-0.00610.22780.04190.202149.372128.556369.1302
41.14360.8346-0.03590.6694-0.06050.187-0.50650.1936-0.2670.0290.1429-0.1356-0.803-0.0627-0.10570.49450.0543-0.09270.28220.04090.148946.014633.799654.6766
50.975-0.9055-0.00150.9756-0.29051.39210.0465-0.0388-0.1843-0.01880.16120.28480.0661-0.22570.84190.1329-0.0326-0.08370.19780.06270.250543.7969.964984.7114
61.019-0.4484-0.12810.7929-0.17320.07520.11580.08950.2252-0.43740.17850.66080.6296-0.13820.1280.4593-0.0236-0.07730.23760.07470.320945.6666-7.770591.0154
70.29940.07050.26610.0145-0.0990.2466-0.09010.2379-0.12870.04870.1523-0.07080.18870.11180.00180.1709-0.0121-0.01510.1794-0.0070.204458.421510.942989.7954
80.0088-0.0694-0.04390.14120.10590.21790.03930.4412-0.13150.11210.1621-0.21860.4480.61020.00060.3078-0.0128-0.04270.2371-0.02390.272859.932-1.930589.858
90.32830.05340.34680.2202-0.210.59490.4250.6378-0.2988-0.92-0.0663-0.0172-0.2666-0.42910.04390.54210.0473-0.12520.3710.01120.263245.20473.488677.9545
101.063-0.69120.89221.3705-0.99491.5942-0.01160.00440.0390.10210.03740.1145-0.08410.0002-0.00070.1458-0.0134-0.01090.1620.00720.173355.219614.693990.3295
110.06320.01260.02590.43830.00330.15230.1674-0.15090.09070.0826-0.0560.04150.09370.0920.00020.2732-0.0169-0.04050.19470.02090.207958.25447.3713101.5398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 154:211)
2X-RAY DIFFRACTION2chain 'A' and (resseq 212:251)
3X-RAY DIFFRACTION3chain 'A' and (resseq 252:314)
4X-RAY DIFFRACTION4chain 'A' and (resseq 315:337)
5X-RAY DIFFRACTION5chain 'B' and (resseq 154:185)
6X-RAY DIFFRACTION6chain 'B' and (resseq 186:197)
7X-RAY DIFFRACTION7chain 'B' and (resseq 198:211)
8X-RAY DIFFRACTION8chain 'B' and (resseq 212:224)
9X-RAY DIFFRACTION9chain 'B' and (resseq 225:242)
10X-RAY DIFFRACTION10chain 'B' and (resseq 243:314)
11X-RAY DIFFRACTION11chain 'B' and (resseq 315:337)

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