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- PDB-2o6g: Crystal structure of IRF-3 bound to the interferon-b enhancer -

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Basic information

Entry
Database: PDB / ID: 2o6g
TitleCrystal structure of IRF-3 bound to the interferon-b enhancer
Components
  • (interferon-b enhancer) x 2
  • Interferon regulatory factor 3
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
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 / 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 cytokine production involved in inflammatory response / positive regulation of type I interferon-mediated 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 / 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 cytokine production involved in inflammatory response / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / mRNA transcription / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / DNA-binding transcription activator activity / cytoplasmic pattern recognition receptor signaling pathway / immune system process / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / antiviral innate immune response / positive regulation of type I interferon production / positive regulation of interferon-alpha 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 / Evasion by RSV of host interferon responses / 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 / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / 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 / innate immune response / 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 / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 / SMAD/FHA domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Interferon regulatory factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPanne, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: An Atomic Model of the Interferon-beta Enhanceosome.
Authors: Panne, D. / Maniatis, T. / Harrison, S.C.
History
DepositionDec 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: interferon-b enhancer
C: interferon-b enhancer
E: Interferon regulatory factor 3
F: Interferon regulatory factor 3
G: Interferon regulatory factor 3
H: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)91,7226
Polymers91,7226
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.020, 105.320, 353.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: DNA chain interferon-b enhancer


Mass: 17844.533 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain interferon-b enhancer


Mass: 17278.072 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein
Interferon regulatory factor 3 / IRF-3


Mass: 14149.879 Da / Num. of mol.: 4 / Fragment: DNA binding domain, residues 3-112
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: 4.82 Å3/Da / Density % sol: 74.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, 20% (w/v) PEG 6000, 500 mM NH4OAc, 100 mM NaCl, 5 mM MgCl2, 5% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris11
2PEG 600011
3NH4OAc11
4NaCl11
5MgCl211
6glycerol11
7HOH11
8Tris12
9PEG 600012
10NH4OAc12
11NaCl12
12MgCl212
13HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2003
Details: bent conical Si-mirror (Rh coating); bent cylindrical Ge(111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 27180 / % possible obs: 87 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.106 / Χ2: 1.21 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.215.40.31726931.0687.9
3.21-3.345.30.31626831.12287.6
3.34-3.495.40.2726891.26587.1
3.49-3.685.40.21326881.29587.1
3.68-3.915.40.15927021.37787
3.91-4.215.50.11527141.27887.2
4.21-4.635.40.09327221.22587.7
4.63-5.35.50.07327451.21287.8
5.3-6.675.50.05727811.10587.7
6.67-505.30.03327631.16583.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.265 1608 5.1 %
Rwork0.251 --
obs-27205 86.9 %
Solvent computationBsol: 47.082 Å2
Displacement parametersBiso mean: 132.235 Å2
Baniso -1Baniso -2Baniso -3
1--10.102 Å20 Å20 Å2
2--5.16 Å20 Å2
3---4.941 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 2331 0 0 5951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.238
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param

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