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- PDB-1qwt: Auto-inhibitory interferon regulation factor-3 (IRF3) transactiva... -

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Basic information

Entry
Database: PDB / ID: 1qwt
TitleAuto-inhibitory interferon regulation factor-3 (IRF3) transactivation domain
ComponentsInterferon regulatory factor 3
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of cytokine production involved in inflammatory response / cGAS/STING signaling pathway ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of cytokine production involved in inflammatory response / cGAS/STING signaling pathway / mRNA transcription / signal transduction involved in regulation of gene expression / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / DNA-binding transcription activator activity / cellular response to exogenous dsRNA / positive regulation of interferon-alpha production / immune system process / positive regulation of type I interferon production / antiviral innate immune response / TICAM1-dependent activation of IRF3/IRF7 / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / 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 / Evasion by RSV of host interferon responses / cellular response to virus / ISG15 antiviral mechanism / DNA-binding transcription repressor activity, RNA polymerase II-specific / Interferon gamma signaling / sequence-specific double-stranded DNA binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / regulation of inflammatory response / TRAF3-dependent IRF activation pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / defense response to virus / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / innate immune response / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / 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 / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsQin, B.Y.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Crystal structure of IRF-3 reveals mechanism of autoinhibition and virus induced phospho-activation
Authors: Qin, B.Y. / Liu, C. / Lam, S.S. / Srinath, H. / Delston, R. / Correia, J.J. / Derynck, R. / Lin, K.
History
DepositionSep 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Interferon regulatory factor 3
B: Interferon regulatory factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,07910
Polymers56,3202
Non-polymers7608
Water9,512528
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.545, 135.545, 68.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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


Mass: 28159.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14653
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
2250 mMammonium phosphate1reservoir
3100 mMBis-Tris1reservoirpH6.0

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. all: 38289 / Num. obs: 36240 / Observed criterion σ(F): 0
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 100 Å / Num. obs: 38291 / % possible obs: 98.8 % / Num. measured all: 244162 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.14 Å / % possible obs: 92.2 % / Num. unique obs: 1737 / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.35

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.1→100 Å / σ(F): 0
RfactorNum. reflection
Rfree0.214 -
Rwork0.195 -
all0.195 36240
obs0.195 36240
Solvent computationBsol: 64.995 Å2 / ksol: 0.342877 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.122 Å2--
2--1.122 Å2-
3----2.243 Å2
Refinement stepCycle: LAST / Resolution: 2.1→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 40 528 4316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005387
X-RAY DIFFRACTIONo_angle_deg1.54035
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0054
X-RAY DIFFRACTIONo_angle_deg1.54

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