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- PDB-5jel: Phosphorylated TRIF in complex with IRF-3 -

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Basic information

Entry
Database: PDB / ID: 5jel
TitlePhosphorylated TRIF in complex with IRF-3
Components
  • Interferon regulatory factor 3
  • Phosphorylated TRIF peptide
KeywordsIMMUNE SYSTEM / Innate Immunity / Signaling
Function / homology
Function and homology information


TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / positive regulation of natural killer cell activation / macrophage apoptotic process / MyD88-independent TLR4 cascade / ripoptosome / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death ...TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / positive regulation of natural killer cell activation / macrophage apoptotic process / MyD88-independent TLR4 cascade / ripoptosome / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of myeloid dendritic cell cytokine production / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / toll-like receptor 3 signaling pathway / TRIF-dependent toll-like receptor signaling pathway / signal transduction involved in regulation of gene expression / RIP-mediated NFkB activation via ZBP1 / macrophage activation involved in immune response / IRF3-mediated induction of type I IFN / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway / positive regulation of cytokine production involved in inflammatory response / cGAS/STING signaling pathway / mRNA transcription / positive regulation of macrophage cytokine production / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / DNA-binding transcription activator activity / toll-like receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / immune system process / cellular response to exogenous dsRNA / response to exogenous dsRNA / B cell proliferation / positive regulation of interferon-alpha production / regulation of protein-containing complex assembly / positive regulation of type I interferon production / positive regulation of autophagy / signaling adaptor activity / positive regulation of chemokine production / positive regulation of B cell proliferation / antiviral innate immune response / lipopolysaccharide-mediated signaling pathway / nitric oxide biosynthetic process / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of interferon-beta production / autophagosome / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / TICAM1, RIP1-mediated IKK complex recruitment / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / apoptotic signaling pathway / promoter-specific chromatin binding / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Evasion by RSV of host interferon responses / DNA-binding transcription repressor activity, RNA polymerase II-specific / ISG15 antiviral mechanism / positive regulation of interleukin-6 production / Interferon gamma signaling / sequence-specific double-stranded DNA binding / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / Interferon alpha/beta signaling / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / sequence-specific DNA binding / molecular adaptor activity / early endosome / DNA-binding transcription factor activity, RNA polymerase II-specific / endosome membrane / endosome / inflammatory response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / innate immune response / DNA damage response / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
TIR domain-containing adapter molecule 1 / TRIF, N-terminal / TRIF N-terminal domain / : / RHIM domain / RIP homotypic interaction motif / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 ...TIR domain-containing adapter molecule 1 / TRIF, N-terminal / TRIF N-terminal domain / : / RHIM domain / RIP homotypic interaction motif / 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 / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily / Tumour Suppressor Smad4 / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / 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 / TIR domain-containing adapter molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsZhao, B. / Li, P.
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
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon regulatory factor 3
B: Phosphorylated TRIF peptide


Theoretical massNumber of molelcules
Total (without water)29,3922
Polymers29,3922
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-9 kcal/mol
Surface area12200 Å2
MethodPISA
2
A: Interferon regulatory factor 3
B: Phosphorylated TRIF peptide

A: Interferon regulatory factor 3
B: Phosphorylated TRIF peptide


Theoretical massNumber of molelcules
Total (without water)58,7844
Polymers58,7844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area4530 Å2
ΔGint-31 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.811, 72.811, 127.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21A-737-

HOH

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Components

#1: Protein Interferon regulatory factor 3 / IRF-3


Mass: 26901.416 Da / Num. of mol.: 1 / 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
#2: Protein/peptide Phosphorylated TRIF peptide


Mass: 2490.421 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IUC6*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaAc pH 4.6, 2.0M NaCl

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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: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→44.848 Å / Num. obs: 52282 / % possible obs: 99.8 % / Redundancy: 11.9 % / Net I/σ(I): 45.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.6→44.848 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.61
RfactorNum. reflection% reflection
Rfree0.1871 2011 3.85 %
Rwork0.1679 --
obs0.1687 52240 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→44.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 0 267 2216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062016
X-RAY DIFFRACTIONf_angle_d1.0392755
X-RAY DIFFRACTIONf_dihedral_angle_d14.083732
X-RAY DIFFRACTIONf_chiral_restr0.044294
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6005-1.64050.2821400.25573525X-RAY DIFFRACTION99
1.6405-1.68490.27291400.22173525X-RAY DIFFRACTION100
1.6849-1.73440.21741420.2013553X-RAY DIFFRACTION100
1.7344-1.79040.2121410.19263510X-RAY DIFFRACTION100
1.7904-1.85440.20061420.18263544X-RAY DIFFRACTION100
1.8544-1.92870.20911420.17183565X-RAY DIFFRACTION100
1.9287-2.01640.18081390.17213563X-RAY DIFFRACTION100
2.0164-2.12270.18081430.16983570X-RAY DIFFRACTION100
2.1227-2.25570.19131420.16863581X-RAY DIFFRACTION100
2.2557-2.42990.18361460.17583600X-RAY DIFFRACTION100
2.4299-2.67440.20751430.18353591X-RAY DIFFRACTION100
2.6744-3.06130.17741490.17673619X-RAY DIFFRACTION100
3.0613-3.85660.18431490.14873672X-RAY DIFFRACTION100
3.8566-44.86610.16471530.14943811X-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)
11.3825-0.1224-0.39981.19590.3051.72370.1146-0.02420.2070.05530.0484-0.2048-0.33820.2624-0.10490.2647-0.0750.02540.1286-0.01460.18339.037376.2505137.9856
20.29070.9264-0.04316.4181-0.24490.0087-0.2570.423-0.2402-1.42190.4897-0.25640.514-0.11-0.1180.4998-0.1308-0.0010.2586-0.05250.31626.575663.4682125.8711
31.42860.67390.19522.19390.56412.16540.0143-0.00270.12350.03180.11340.1448-0.1697-0.1537-0.1020.1855-0.00330.02420.10620.01930.1518-2.551573.5248140.1572
43.584-0.36562.02815.4460.62681.27620.0367-0.72360.40840.62060.1312-0.6044-0.89141.0928-0.1690.443-0.2083-0.01650.6303-0.16240.41216.448383.6407152.6151
51.4907-0.35070.03122.99610.34821.34280.2045-0.29820.6928-0.04690.0737-0.1591-0.80530.16230.04190.7959-0.13240.13320.3371-0.19320.51426.743292.6213152.631
65.74781.67942.06675.0455-5.15129.3323-0.1574-0.2627-0.25370.29880.52961.63870.3422-0.993-0.3610.2883-0.10670.04650.2764-0.00470.3463-14.694355.5182133.0059
72.3068-3.81892.54146.6207-4.56873.238-0.22441.35560.5867-1.441-0.1740.04880.3982-0.09350.42210.5446-0.1432-0.06310.49890.09530.2912-11.01565.6488122.8188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 189 through 229 )
2X-RAY DIFFRACTION2chain 'A' and (resid 230 through 254 )
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 383 )
4X-RAY DIFFRACTION4chain 'A' and (resid 384 through 400 )
5X-RAY DIFFRACTION5chain 'A' and (resid 401 through 422 )
6X-RAY DIFFRACTION6chain 'B' and (resid 199 through 206 )
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 212 )

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