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- PDB-5jej: Phosphorylated STING in complex with IRF-3 CTD -

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Basic information

Entry
Database: PDB / ID: 5jej
TitlePhosphorylated STING in complex with IRF-3 CTD
Components
  • Interferon regulatory factor 3IRF3
  • Stimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / Innate Immunity / Signaling
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / STING complex / STAT6-mediated induction of chemokines / programmed necrotic cell death / serine/threonine protein kinase complex / 2',3'-cyclic GMP-AMP binding / proton channel activity / TRIF-dependent toll-like receptor signaling pathway ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / STING complex / STAT6-mediated induction of chemokines / programmed necrotic cell death / serine/threonine protein kinase complex / 2',3'-cyclic GMP-AMP binding / proton channel activity / TRIF-dependent toll-like receptor signaling pathway / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / cGAS/STING signaling pathway / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / mRNA transcription / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / pattern recognition receptor signaling pathway / DNA-binding transcription activator activity / immune system process / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / autophagosome membrane / positive regulation of interferon-alpha production / antiviral innate immune response / positive regulation of macroautophagy / autophagosome assembly / cellular response to organic cyclic compound / positive regulation of type I interferon production / autophagosome / cellular response to interferon-beta / signaling adaptor activity / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / TICAM1-dependent activation of IRF3/IRF7 / Regulation of innate immune responses to cytosolic DNA / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / secretory granule membrane / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cytoplasmic vesicle membrane / ISG15 antiviral mechanism / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / peroxisome / positive regulation of DNA-binding transcription factor activity / SARS-CoV-1 activates/modulates innate immune responses / Interferon gamma signaling / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / positive regulation of protein binding / protein complex oligomerization / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / regulation of apoptotic process / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / endosome / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / Golgi membrane / innate immune response / apoptotic process / ubiquitin protein ligase binding / DNA damage response / chromatin / Neutrophil degranulation / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / 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 / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain ...Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interferon regulatory factor 3 / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, P. / Shu, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins.
Authors: Zhao, B. / Shu, C. / Gao, X. / Sankaran, B. / Du, F. / Shelton, C.L. / Herr, A.B. / Ji, J.Y. / Li, P.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Stimulator of interferon genes protein
D: Stimulator of interferon genes protein
E: Stimulator of interferon genes protein
A: Interferon regulatory factor 3
B: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)66,5405
Polymers66,5405
Non-polymers00
Water6,846380
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.076, 56.401, 75.548
Angle α, β, γ (deg.)90.00, 104.64, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-657-

HOH

21B-673-

HOH

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Components

#1: Protein/peptide 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: 4245.697 Da / Num. of mol.: 3 / Fragment: UNP residues 342-379
Source method: isolated from a genetically manipulated source
Details: Phosphoserine included in the structure / 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: Protein Interferon regulatory factor 3 / IRF3 / IRF-3


Mass: 26901.416 Da / Num. of mol.: 2 / Fragment: UNP residues 189-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14653
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris, pH 5.5, 200 mM MgCl2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.654 Å / Num. obs: 35085 / % possible obs: 98.2 % / Redundancy: 3.6 % / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.654 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.76
RfactorNum. reflection% reflection
Rfree0.2373 1998 5.7 %
Rwork0.1762 --
obs0.1797 35068 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→44.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3961 0 0 380 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074072
X-RAY DIFFRACTIONf_angle_d1.0045552
X-RAY DIFFRACTIONf_dihedral_angle_d14.7911481
X-RAY DIFFRACTIONf_chiral_restr0.041592
X-RAY DIFFRACTIONf_plane_restr0.005719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9948-2.04470.35171200.27291997X-RAY DIFFRACTION84
2.0447-2.10.33431350.25032226X-RAY DIFFRACTION93
2.1-2.16180.28681420.23812321X-RAY DIFFRACTION98
2.1618-2.23160.32311430.23072386X-RAY DIFFRACTION99
2.2316-2.31130.3191430.23862382X-RAY DIFFRACTION100
2.3113-2.40390.25271450.1922389X-RAY DIFFRACTION100
2.4039-2.51320.26031460.19032409X-RAY DIFFRACTION100
2.5132-2.64570.25171440.1842397X-RAY DIFFRACTION100
2.6457-2.81150.27541450.18162389X-RAY DIFFRACTION100
2.8115-3.02850.26911460.18752421X-RAY DIFFRACTION100
3.0285-3.33320.24511450.17742403X-RAY DIFFRACTION100
3.3332-3.81530.19571460.14492406X-RAY DIFFRACTION100
3.8153-4.8060.19211480.12972448X-RAY DIFFRACTION100
4.806-44.66490.18391500.1572496X-RAY DIFFRACTION100
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)
14.51121.45082.86269.9936-0.62167.03890.2381-0.6242-0.7021.21350.07960.00810.76040.3404-0.31350.48190.0899-0.01620.6580.15880.342787.2329.1452399.6199
20.2824-0.34210.5261.37111.13384.2589-0.05510.4116-1.4677-0.4816-0.8614-1.8338-0.40630.37890.91550.42860.010.12220.45890.07670.887881.957215.8712409.8534
32.1516-0.27510.47629.26920.56416.44540.7745-1.41911.3330.46760.0258-0.3304-1.04550.5357-0.80110.3987-0.00710.02430.423-0.12360.3171111.148768.1908394.3349
42.74791.4096-3.99135.8302-5.61058.2834-0.1912-0.2053-0.65760.0727-0.3916-0.70660.36320.22620.58080.42140.1048-0.01060.98190.06210.5737103.053431.0636392.164
52.1952-1.5454-0.68133.58960.38961.55940.1080.3774-0.0949-0.2472-0.1038-0.0164-0.0242-0.1074-0.00490.1949-0.0232-0.02580.3329-0.01360.1753112.916550.209372.547
69.9785-8.1322-4.28347.77763.58914.39270.279-0.63391.6651-0.25890.2972-0.866-0.58260.3609-0.58510.2615-0.0076-0.02630.3988-0.01030.4035110.861567.43375.4124
71.23850.28640.07533.09371.13921.2739-0.0192-0.1018-0.04820.11110.0107-0.00150.04160.0573-0.01150.123-0.0019-0.00870.24740.01970.1254111.932545.7267381.1962
83.578-2.12140.49462.6560.28650.77740.27410.2328-0.0054-0.2935-0.25760.08030.0426-0.0792-0.02570.17670.00530.01710.26770.02340.156778.619849.0547378.3988
92.0017-9.0962-1.75216.09831.19950.5136-0.0382-0.0342-1.98960.0073-0.10070.77560.5444-0.17130.13890.3069-0.028-0.01810.34270.06110.450482.379131.6161379.7344
101.9321-1.5320.34334.9232-0.73891.4189-0.0156-0.4566-0.15840.28690.0740.16430.10.0281-0.03070.1789-0.01670.01880.34310.03320.136481.78642.2408390.8708
111.3471-0.69150.06172.3154-0.95711.0308-0.0545-0.15560.21830.1643-0.0202-0.0819-0.12750.05270.07910.147-0.0263-0.01970.2824-0.0350.178783.041860.0114383.177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 359 through 371 )
2X-RAY DIFFRACTION2chain 'C' and (resid 372 through 379 )
3X-RAY DIFFRACTION3chain 'D' and (resid 359 through 368 )
4X-RAY DIFFRACTION4chain 'E' and (resid 376 through 379 )
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 254 )
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 422 )
8X-RAY DIFFRACTION8chain 'B' and (resid 189 through 229 )
9X-RAY DIFFRACTION9chain 'B' and (resid 230 through 254 )
10X-RAY DIFFRACTION10chain 'B' and (resid 255 through 316 )
11X-RAY DIFFRACTION11chain 'B' and (resid 317 through 421 )

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