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- PDB-4emu: Crystal structure of ligand free human STING -

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Basic information

Entry
Database: PDB / ID: 4emu
TitleCrystal structure of ligand free human STING
ComponentsTransmembrane protein 173Stimulator of interferon genes
KeywordsMEMBRANE PROTEIN / alpha/beta fold / innate immune sensor / c-di-GMP
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / 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 / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / 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 / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / autophagosome assembly / cellular response to organic cyclic compound / autophagosome / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / secretory granule membrane / cytoplasmic vesicle membrane / positive regulation of DNA-binding transcription factor activity / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein complex oligomerization / 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 / Transmembrane protein 173 / 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 / Transmembrane protein 173 / 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 / FOURIER SYNTHESIS / Resolution: 1.9 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 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
B: Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0883
Polymers43,0482
Non-polymers401
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-19 kcal/mol
Surface area18040 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)86,1776
Polymers86,0974
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area4360 Å2
ΔGint-54 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.931, 78.108, 127.768
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-556-

HOH

21B-572-

HOH

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Components

#1: Protein Transmembrane protein 173 / Stimulator of interferon genes / 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: 21524.158 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-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M HEPES, pH 8.5, 28% PEG400, 0.2M CaCl2, 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: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2012 / Details: Si Crystal
RadiationMonochromator: Si Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→39 Å / Num. all: 27829 / Num. obs: 27829 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.674 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→37.348 Å / SU ML: 0.57 / σ(F): 1.34 / σ(I): 0 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 2000 7.2 %Random
Rwork0.2106 ---
obs0.2133 27787 99.4 %-
all-27787 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.256 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-19.5924 Å2-0 Å2-0 Å2
2---9.155 Å20 Å2
3----10.4374 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 1 146 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062884
X-RAY DIFFRACTIONf_angle_d1.0633910
X-RAY DIFFRACTIONf_dihedral_angle_d14.9161088
X-RAY DIFFRACTIONf_chiral_restr0.073428
X-RAY DIFFRACTIONf_plane_restr0.004518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.40241440.32371842X-RAY DIFFRACTION99
1.9475-2.00020.30931400.29121818X-RAY DIFFRACTION100
2.0002-2.0590.33731400.26551812X-RAY DIFFRACTION100
2.059-2.12550.33071410.24991812X-RAY DIFFRACTION99
2.1255-2.20140.2911420.22271837X-RAY DIFFRACTION100
2.2014-2.28960.27261410.20821809X-RAY DIFFRACTION100
2.2896-2.39380.28421420.2181842X-RAY DIFFRACTION100
2.3938-2.51990.24091430.21121831X-RAY DIFFRACTION100
2.5199-2.67780.25751430.21961841X-RAY DIFFRACTION100
2.6778-2.88450.31011420.22951844X-RAY DIFFRACTION99
2.8845-3.17460.23781430.21251838X-RAY DIFFRACTION100
3.1746-3.63360.251450.20371869X-RAY DIFFRACTION99
3.6336-4.57670.20691450.17331857X-RAY DIFFRACTION99
4.5767-37.35540.21051490.20751935X-RAY DIFFRACTION98
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)
10.34510.436-0.16910.446-0.33320.22240.11540.1006-0.3264-0.135-0.29740.16420.37770.9426-0.04350.40530.3895-0.12890.57230.01890.247458.407719.862260.1062
20.00720.06090.00240.191-0.14590.09160.0828-0.0717-0.04240.3429-0.33030.11310.7731-0.1373-0.04290.66440.1157-0.05390.3685-0.02320.422646.746718.034159.3732
31.0835-0.17820.67950.4254-0.86050.97790.1951-0.024-0.16870.0544-0.03870.1150.03020.28880.09550.23540.0296-0.04110.29360.06180.253149.392627.899666.2946
40.02690.00740.09610.01820.01780.18620.17590.31390.2043-0.1031-0.1983-0.0568-0.2426-0.06370.00010.45320.07430.00150.37470.01670.254246.156733.908754.6062
50.7847-0.0094-0.39050.18790.17212.0310.2196-0.1402-0.1710.02350.38310.3469-0.7606-0.91550.5982-0.2248-0.1324-0.27580.41490.23950.46844.15719.749684.1215
6-0.03250.07980.11210.13830.11330.4195-0.18810.1362-0.1091-0.190.36290.18310.29480.06080.03830.3304-0.0244-0.02630.21040.06320.3454.991.624190.1311
70.30420.0159-0.18720.10930.11290.19470.07530.0387-0.1664-0.1840.07820.12260.49140.13210.00040.4216-0.0601-0.11320.22220.04880.440952.9584-0.776988.0365
80.5719-0.46290.55080.4987-0.42220.3993-0.1441-0.02370.2160.19450.08240.133-0.4060.0303-00.2820.0126-0.0240.23020.0450.249455.384920.390688.704
90.0659-0.07640.05320.11110.00420.17470.0674-0.11930.0237-0.04810.08970.14760.1668-0.0135-0.00120.33980.02050.00610.30670.08590.30858.2267.0688100.7765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 154:203)
2X-RAY DIFFRACTION2chain 'A' and (resseq 204:241)
3X-RAY DIFFRACTION3chain 'A' and (resseq 242:314)
4X-RAY DIFFRACTION4chain 'A' and (resseq 315:337)
5X-RAY DIFFRACTION5chain 'B' and (resseq 154:185)
6X-RAY DIFFRACTION6chain 'B' and (resseq 186:218)
7X-RAY DIFFRACTION7chain 'B' and (resseq 219:262)
8X-RAY DIFFRACTION8chain 'B' and (resseq 263:314)
9X-RAY DIFFRACTION9chain 'B' and (resseq 315:337)

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