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- PDB-5jeo: Phosphorylated Rotavirus NSP1 in complex with IRF-3 -

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Basic information

Entry
Database: PDB / ID: 5jeo
TitlePhosphorylated Rotavirus NSP1 in complex with IRF-3
Components
  • Interferon regulatory factor 3
  • Rotavirus NSP1 peptide
KeywordsIMMUNE SYSTEM / Viral Immuinity
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cytoskeleton / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / signal transduction involved in regulation of gene expression / IRF3-mediated induction of type I IFN / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cytoskeleton / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / signal transduction involved in regulation of gene expression / 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 / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / DNA-binding transcription activator activity / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / immune system process / cellular response to exogenous dsRNA / positive regulation of interferon-alpha production / positive regulation of type I interferon production / antiviral innate immune response / lipopolysaccharide-mediated signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of interferon-beta production / Regulation of innate immune responses to cytosolic DNA / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / Interferon gamma signaling / sequence-specific double-stranded DNA binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / 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 / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / sequence-specific DNA binding / host cell cytoplasm / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / innate immune response / virus-mediated perturbation of host defense response / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / 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 / nucleus / metal ion binding / 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 / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / 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
PHOSPHATE ION / Interferon regulatory factor 3 / Non-structural protein 1
Similarity search - Component
Biological speciesRotavirus A
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.719 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 16, 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
B: Rotavirus NSP1 peptide
A: Interferon regulatory factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5245
Polymers29,2392
Non-polymers2853
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-24 kcal/mol
Surface area11950 Å2
MethodPISA
2
B: Rotavirus NSP1 peptide
A: Interferon regulatory factor 3
hetero molecules

B: Rotavirus NSP1 peptide
A: Interferon regulatory factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,04710
Polymers58,4774
Non-polymers5706
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5920 Å2
ΔGint-71 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.982, 72.982, 127.551
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-643-

HOH

21A-797-

HOH

31A-805-

HOH

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Components

#1: Protein/peptide Rotavirus NSP1 peptide


Mass: 2337.297 Da / Num. of mol.: 1
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 / 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH7.5, 0.8 M NaH2PO4, 0.8 M KH2PO4

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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 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.719→44.893 Å / Num. obs: 42593 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / CC1/2: 0.823 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/av σ(I): 44.5 / Net I/σ(I): 44.5
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.719→44.893 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 2001 4.7 %
Rwork0.1691 --
obs0.1698 42536 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.719→44.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 15 216 2157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072043
X-RAY DIFFRACTIONf_angle_d1.0052795
X-RAY DIFFRACTIONf_dihedral_angle_d13.923741
X-RAY DIFFRACTIONf_chiral_restr0.046296
X-RAY DIFFRACTIONf_plane_restr0.005364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7192-1.76220.29491390.26632845X-RAY DIFFRACTION99
1.7622-1.80980.29641380.252852X-RAY DIFFRACTION100
1.8098-1.86310.24411430.21382882X-RAY DIFFRACTION100
1.8631-1.92320.21061370.18672837X-RAY DIFFRACTION100
1.9232-1.99190.22491440.18072870X-RAY DIFFRACTION100
1.9919-2.07170.20771420.18222860X-RAY DIFFRACTION100
2.0717-2.1660.20821410.18152874X-RAY DIFFRACTION100
2.166-2.28020.17631450.1732868X-RAY DIFFRACTION100
2.2802-2.4230.21441400.17032887X-RAY DIFFRACTION100
2.423-2.61010.19591450.17122906X-RAY DIFFRACTION100
2.6101-2.87270.17481430.17392880X-RAY DIFFRACTION100
2.8727-3.28830.17681430.17192927X-RAY DIFFRACTION100
3.2883-4.14240.15851440.14952949X-RAY DIFFRACTION100
4.1424-44.90810.16241570.15433098X-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)
13.4525-3.7133.34314.7392-3.50183.2792-0.75480.4782-0.0608-1.25160.65460.6360.2092-0.6457-0.16950.5019-0.1557-0.10170.41190.0120.3498-48.6239-2.3104-0.9385
21.2189-0.3702-0.72241.1086-0.03111.8828-0.0020.13150.2122-0.13190.1771-0.2485-0.50830.3648-0.11510.306-0.1251-0.00030.2056-0.00210.2148-28.295812.606610.3077
30.50531.0102-0.25049.4612-5.04263.3125-0.20990.2837-0.1704-1.08240.069-0.56890.43150.16750.07360.4233-0.09240.03910.313-0.0470.2844-30.4572-0.2951-1.1737
40.98540.46630.33872.66970.8112.7322-0.15040.11580.1666-0.1530.22040.2525-0.333-0.1329-0.050.2223-0.0291-0.01060.16650.03750.2268-40.322110.889510.3194
52.26880.4441-0.29333.97350.55623.5744-0.0163-0.16870.38440.29130.2554-0.1561-0.72760.4312-0.09980.333-0.04430.020.1574-0.03080.2333-32.057916.89521.31
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 482 through 491 )
2X-RAY DIFFRACTION2chain 'A' and (resid 189 through 229 )
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 254 )
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 348 )
5X-RAY DIFFRACTION5chain 'A' and (resid 349 through 422 )

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