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- PDB-4f9g: Crystal structure of STING complex with Cyclic di-GMP. -

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Basic information

Entry
Database: PDB / ID: 4f9g
TitleCrystal structure of STING complex with Cyclic di-GMP.
ComponentsTransmembrane protein 173
KeywordsPROTEIN BINDING / INTERFERON / IMMUNE SYSTEM C-DI-GMP Dimerisation
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / 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 / cytoplasmic vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / positive regulation of interferon-beta production / autophagosome / secretory granule membrane / positive regulation of DNA-binding transcription factor activity / SARS-CoV-1 activates/modulates innate immune responses / peroxisome / positive regulation of protein binding / regulation of inflammatory response / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / 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 / : / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsKabaleeswaran, V. / Wu, H.
CitationJournal: Mol.Cell / Year: 2012
Title: Cyclic di-GMP Sensing via the Innate Immune Signaling Protein STING.
Authors: Yin, Q. / Tian, Y. / Kabaleeswaran, V. / Jiang, X. / Tu, D. / Eck, M.J. / Chen, Z.J. / Wu, H.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Other
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
C: Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3873
Polymers59,6972
Non-polymers6901
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-16 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.027, 74.200, 60.013
Angle α, β, γ (deg.)90.000, 96.320, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEUchain 'A' and (resseq 154:189 or resseq 191:226 or resseq...AA154 - 18940 - 75
12ARGARGPROPROchain 'A' and (resseq 154:189 or resseq 191:226 or resseq...AA191 - 22677 - 112
13SERSERPROPROchain 'A' and (resseq 154:189 or resseq 191:226 or resseq...AA241 - 303127 - 189
14ASNASNCYSCYSchain 'A' and (resseq 154:189 or resseq 191:226 or resseq...AA307 - 309193 - 195
15LEULEUPROPROchain 'A' and (resseq 154:189 or resseq 191:226 or resseq...AA311 - 317197 - 203
16SERSERVALVALchain 'A' and (resseq 154:189 or resseq 191:226 or resseq...AA322 - 343208 - 229
21ASNASNLEULEUchain 'C' and (resseq 154:189 or resseq 191:226 or resseq...CB154 - 18940 - 75
22ARGARGPROPROchain 'C' and (resseq 154:189 or resseq 191:226 or resseq...CB191 - 22677 - 112
23SERSERPROPROchain 'C' and (resseq 154:189 or resseq 191:226 or resseq...CB241 - 303127 - 189
24ASNASNCYSCYSchain 'C' and (resseq 154:189 or resseq 191:226 or resseq...CB307 - 309193 - 195
25LEULEUPROPROchain 'C' and (resseq 154:189 or resseq 191:226 or resseq...CB311 - 317197 - 203
26PHEPHEVALVALchain 'C' and (resseq 154:189 or resseq 191:226 or resseq...CB323 - 343209 - 229

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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.: 2 / Fragment: C-terminal Domain (unp residues 139-379)
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) / Strain (production host): bl21-de3 / 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

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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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12-15% PEG8000, 0.08 M sodium cacodylate pH 6.3-6.5, 0.16 M calcium acetate and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 11107 / % possible obs: 98.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.066 / Χ2: 1.901 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.065.90.48511111.3841100
3.06-3.185.90.34911201.3851100
3.18-3.325.90.22311231.51100
3.32-3.55.90.15311031.6211100
3.5-3.725.90.10911291.7471100
3.72-45.90.07511231.984199.7
4-4.415.80.05910902.248199.5
4.41-5.045.70.05311232.599198.3
5.04-6.355.60.04611192.306199.6
6.35-505.30.03510662.382191.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F9E

4f9e


Resolution: 2.95→38.298 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7655 / SU ML: 0.38 / σ(F): 1.38 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 1089 9.83 %random
Rwork0.2049 ---
obs0.2099 11082 98.47 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.096 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 160.69 Å2 / Biso mean: 91.8595 Å2 / Biso min: 52.41 Å2
Baniso -1Baniso -2Baniso -3
1-15.7208 Å2-0 Å2-30.0074 Å2
2---28.5616 Å20 Å2
3---12.8408 Å2
Refinement stepCycle: LAST / Resolution: 2.95→38.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 46 0 2720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112775
X-RAY DIFFRACTIONf_angle_d1.5343778
X-RAY DIFFRACTIONf_chiral_restr0.089427
X-RAY DIFFRACTIONf_plane_restr0.006485
X-RAY DIFFRACTIONf_dihedral_angle_d17.5721014
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1289X-RAY DIFFRACTIONPOSITIONAL0.038
12C1289X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9431-3.0770.34331390.26891240137998
3.077-3.23910.32181410.25312321373100
3.2391-3.44190.28461440.202112621406100
3.4419-3.70750.24291310.185612651396100
3.7075-4.08020.25681090.16311280138999
4.0802-4.66970.23381630.17591245140899
4.6697-5.87990.2261280.20041263139199
5.8799-38.3010.25961340.2391206134093

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