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- PDB-5jer: Structure of Rotavirus NSP1 bound to IRF-3 -

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Basic information

Entry
Database: PDB / ID: 5jer
TitleStructure of Rotavirus NSP1 bound to IRF-3
Components
  • Interferon regulatory factor 3IRF3
  • Rotavirus NSP1 peptide
KeywordsIMMUNE SYSTEM / Viral Immunity
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / macrophage apoptotic process / host cytoskeleton / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / macrophage apoptotic process / host cytoskeleton / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / mRNA transcription / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / 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 / positive regulation of interferon-alpha production / antiviral innate immune response / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / ISG15 antiviral mechanism / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / SARS-CoV-1 activates/modulates innate immune responses / Interferon gamma signaling / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / host cell cytoplasm / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / apoptotic process / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rotavirus non-structural protein 1 / Rotavirus RNA-binding Protein 53 (NS53) / 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 ...Rotavirus non-structural protein 1 / Rotavirus RNA-binding Protein 53 (NS53) / 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 / 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 / Non-structural protein 1
Similarity search - Component
Biological speciesRotavirus A
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.913 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 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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
B: Rotavirus NSP1 peptide
D: Rotavirus NSP1 peptide
F: Rotavirus NSP1 peptide
H: Rotavirus NSP1 peptide
A: Interferon regulatory factor 3
C: Interferon regulatory factor 3
E: Interferon regulatory factor 3
G: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)116,6358
Polymers116,6358
Non-polymers00
Water0
1
B: Rotavirus NSP1 peptide
A: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)29,1592
Polymers29,1592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-7 kcal/mol
Surface area12160 Å2
MethodPISA
2
D: Rotavirus NSP1 peptide
C: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)29,1592
Polymers29,1592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-7 kcal/mol
Surface area12000 Å2
MethodPISA
3
F: Rotavirus NSP1 peptide
E: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)29,1592
Polymers29,1592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-7 kcal/mol
Surface area11850 Å2
MethodPISA
4
H: Rotavirus NSP1 peptide
G: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)29,1592
Polymers29,1592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-7 kcal/mol
Surface area11890 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-49 kcal/mol
Surface area41570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.772, 107.924, 135.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
Rotavirus NSP1 peptide


Mass: 2257.318 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99FX5*PLUS
#2: Protein
Interferon regulatory factor 3 / IRF3 / IRF-3


Mass: 26901.416 Da / Num. of mol.: 4 / 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

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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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 5.5, 200 mM MgCl2, 23% 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: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→47.94 Å / Num. obs: 22409 / % possible obs: 100 % / Redundancy: 7.1 % / Net I/σ(I): 15.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.913→47.94 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1
RfactorNum. reflection% reflection
Rfree0.2503 1998 8.94 %
Rwork0.2096 --
obs0.2133 22342 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.913→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 0 0 0 7688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027935
X-RAY DIFFRACTIONf_angle_d0.58910815
X-RAY DIFFRACTIONf_dihedral_angle_d14.4852875
X-RAY DIFFRACTIONf_chiral_restr0.0231157
X-RAY DIFFRACTIONf_plane_restr0.0031410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.913-2.98540.34531320.31091354X-RAY DIFFRACTION95
2.9854-3.06610.31911410.30251439X-RAY DIFFRACTION100
3.0661-3.15630.3141410.27461435X-RAY DIFFRACTION100
3.1563-3.25820.28871420.25121442X-RAY DIFFRACTION100
3.2582-3.37460.29381410.25331439X-RAY DIFFRACTION100
3.3746-3.50970.26871390.21851418X-RAY DIFFRACTION100
3.5097-3.66940.26591420.2211444X-RAY DIFFRACTION100
3.6694-3.86280.25891430.21061459X-RAY DIFFRACTION100
3.8628-4.10470.22471420.19421453X-RAY DIFFRACTION100
4.1047-4.42140.23651430.18661452X-RAY DIFFRACTION100
4.4214-4.86590.20481450.17051469X-RAY DIFFRACTION100
4.8659-5.56910.20931440.17881467X-RAY DIFFRACTION100
5.5691-7.0130.25611480.20461497X-RAY DIFFRACTION100
7.013-47.94670.22151550.1831576X-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)
12.76641.5413-0.61761.25790.38862.87220.79491.2402-1.0677-0.5284-0.31510.12960.619-0.07720.18210.67160.05080.19520.5543-0.15660.5771150.3238413.83294.3607
22.0794-0.42581.04452.43680.15353.7572-0.3492-0.62211.21490.1751-0.1739-0.3385-0.69520.06030.20130.5966-0.0393-0.07110.4981-0.02960.4773144.6759449.806166.4574
34.83540.4880.00215.351.33413.5640.34470.7580.9518-0.71340.13171.1791-0.65190.2244-0.40440.57570.063-0.03680.66020.17780.5926128.792451.76787.1977
46.4999-1.83331.1345.064-0.72025.11460.3901-0.7703-1.21380.49560.06960.20160.0772-0.3499-0.79040.4151-0.04450.02810.5438-0.01570.4233124.1451410.982566.1065
52.61791.73-0.3886.85712.06092.00270.1207-1.146-0.1223-0.2761-0.3076-1.1297-0.09080.0187-0.31620.31420.0120.04550.43250.02710.3317159.8513436.603927.2227
65.7675-0.32941.11851.56810.99453.7411-0.07980.6208-0.36230.3109-0.0331-0.50731.20870.53840.09060.49520.18590.05850.4560.10820.2881156.8469420.348224.6428
77.2655-3.04490.29214.3138-0.49084.2287-0.40080.2034-2.8905-0.3758-0.49771.12761.1518-0.48540.61150.9969-0.06940.36790.34080.00210.6013144.1142410.801716.106
82.7355-0.2522-0.10240.5224-1.22562.58870.25250.3214-0.04060.37840.1944-0.13290.63020.367-0.09620.31610.09350.24980.3390.09990.4852160.8408427.027214.4811
95.0009-0.2356-0.78122.53-0.07433.38330.5950.35080.4202-0.9569-0.1124-0.55-0.22380.4402-0.29680.29490.01110.21550.43010.0040.4272154.3993430.67529.7139
102.09020.40330.06574.05551.38252.1146-0.0076-0.23150.43950.10350.0378-0.1154-0.28920.0571-0.0220.31540.01890.11710.2955-0.0030.3135153.7457442.159520.5566
112.2055-0.8092-0.20985.40770.02431.730.04670.90180.0158-0.4346-0.1901-0.6038-0.0287-0.01890.04950.2585-0.0754-0.04160.3542-0.05030.2297150.0562430.370245.5208
121.9329-1.6854-0.49062.2548-0.03835.06270.27760.44140.7254-0.6013-0.2615-0.8705-1.389-0.00270.09430.6328-0.13460.04310.54390.04060.5902157.2336444.545146.8659
133.6017-0.0362-1.53043.34950.74263.48320.07940.12690.1405-0.1134-0.03530.0969-0.6651-0.026-0.05560.3431-0.0844-0.1110.33390.04610.3491148.5328442.898155.1459
146.81351.81441.68792.39121.01712.15040.337-0.6405-1.15680.7456-0.0791-0.91050.25470.1988-0.14040.2986-0.0197-0.06210.30250.06970.5156149.1806432.68462.1482
151.446-0.5175-0.53584.49611.33592.8401-0.19340.0126-0.4832-0.15980.0497-0.12220.4911-0.0610.12870.3483-0.0549-0.01190.2842-0.00790.389148.4708420.83851.4461
162.7531.1302-0.70886.75480.70841.73470.0492-0.36610.50211.3058-0.58611.4253-0.27790.09440.08820.3774-0.0364-0.08440.463-0.04820.5216114.0452420.86628.5572
175.68450.0288-0.86062.98-0.74223.32680.4588-0.45480.64150.57650.0670.3274-0.9417-0.5847-0.35670.40490.17540.12720.3457-0.01190.2317124.0154441.238425.315
186.06150.4193-1.35653.5625-1.02713.76690.3651-0.50871.15010.6739-0.2843-0.4197-0.91580.0566-0.26820.49610.02110.0140.453-0.02050.3731132.4449.143125.032
192.41880.41940.26293.0397-0.60352.33710.00740.31970.3477-0.19450.05740.2615-0.206-0.3518-0.01120.23180.05850.00290.3543-0.00290.3278122.6311442.198115.8704
202.61691.5901-0.79853.262-1.1542.892-0.32420.4454-0.3948-0.76490.260.01320.5675-0.45020.11930.4206-0.08160.04140.4386-0.0890.2727123.0398426.569412.2919
212.87612.3720.66.5669-1.12032.1012-0.06110.2215-0.4214-1.16940.0305-0.00010.63220.03760.24610.4553-0.1110.07680.37140.02130.2113128.3134426.393714.1777
222.34131.0396-1.05464.9545-1.10312.8215-0.1825-0.1384-0.3241-0.0663-0.0173-0.42030.53230.19670.11630.26620.00310.02290.319-0.0190.2112129.2926425.852321.18
232.96370.69290.80883.8336-0.9584.41260.259-0.183-0.4947-0.3934-0.01970.36080.5425-1.02660.00010.6837-0.09080.04720.4915-0.03110.4584117.3984411.011921.6619
241.24290.5103-0.83853.27391.0490.91440.40140.6481-0.0853-0.5388-0.49130.51060.1-0.34430.07870.2668-0.03620.01230.4849-0.00120.2274117.1132429.310246.0297
255.3061-1.45970.61483.4861-1.17912.46030.275-0.7597-0.86610.2251-0.2323-0.0510.9933-0.483-0.03680.5609-0.07460.05780.3561-0.05330.4024120.7406412.229447.853
262.0162-0.6293-0.42641.8633-0.87142.98430.1067-0.3674-0.23710.2665-0.24990.33080.2593-0.34820.13280.225-0.05330.10390.4607-0.10630.3794118.3991422.375258.7356
271.37410.17410.07713.67140.11351.4648-0.0452-0.03110.30370.2978-0.08260.3922-0.5226-0.1450.0870.26560.05140.08390.3921-0.07590.2981119.7491440.460852.0982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 482 through 491 )
2X-RAY DIFFRACTION2chain 'D' and (resid 482 through 491 )
3X-RAY DIFFRACTION3chain 'F' and (resid 482 through 491 )
4X-RAY DIFFRACTION4chain 'H' and (resid 482 through 491 )
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 210 )
6X-RAY DIFFRACTION6chain 'A' and (resid 211 through 244 )
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 267 )
8X-RAY DIFFRACTION8chain 'A' and (resid 268 through 296 )
9X-RAY DIFFRACTION9chain 'A' and (resid 297 through 316 )
10X-RAY DIFFRACTION10chain 'A' and (resid 317 through 422 )
11X-RAY DIFFRACTION11chain 'C' and (resid 189 through 220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 221 through 240 )
13X-RAY DIFFRACTION13chain 'C' and (resid 241 through 296 )
14X-RAY DIFFRACTION14chain 'C' and (resid 297 through 316 )
15X-RAY DIFFRACTION15chain 'C' and (resid 317 through 422 )
16X-RAY DIFFRACTION16chain 'E' and (resid 189 through 203 )
17X-RAY DIFFRACTION17chain 'E' and (resid 204 through 240 )
18X-RAY DIFFRACTION18chain 'E' and (resid 241 through 254 )
19X-RAY DIFFRACTION19chain 'E' and (resid 255 through 296 )
20X-RAY DIFFRACTION20chain 'E' and (resid 297 through 334 )
21X-RAY DIFFRACTION21chain 'E' and (resid 335 through 348 )
22X-RAY DIFFRACTION22chain 'E' and (resid 349 through 400 )
23X-RAY DIFFRACTION23chain 'E' and (resid 401 through 422 )
24X-RAY DIFFRACTION24chain 'G' and (resid 189 through 229 )
25X-RAY DIFFRACTION25chain 'G' and (resid 230 through 254 )
26X-RAY DIFFRACTION26chain 'G' and (resid 255 through 316 )
27X-RAY DIFFRACTION27chain 'G' and (resid 317 through 422 )

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