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- PDB-1j2f: X-ray crystal structure of IRF-3 and its functional implications -

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Basic information

Entry
Database: PDB / ID: 1j2f
TitleX-ray crystal structure of IRF-3 and its functional implications
ComponentsInterferon regulatory factor 3
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION FACTOR
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 / positive regulation of type I interferon-mediated signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / 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 / positive regulation of type I interferon-mediated signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / positive regulation of cytokine production involved in inflammatory response / cGAS/STING signaling pathway / signal transduction involved in regulation of gene expression / mRNA transcription / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / DNA-binding transcription activator activity / cytoplasmic pattern recognition receptor signaling pathway / 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 / TRAF3-dependent IRF activation pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response / regulation of apoptotic process / defense response to virus / sequence-specific DNA binding / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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
Interferon regulatory factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsTakahasi, K. / Noda, N. / Horiuchi, M. / Mori, M. / Okabe, Y. / Fukuhara, Y. / Terasawa, H. / Fujita, T. / Inagaki, F.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: X-ray crystal structure of IRF-3 and its functional implications.
Authors: Takahasi, K. / Suzuki, N.N. / Horiuchi, M. / Mori, M. / Suhara, W. / Okabe, Y. / Fukuhara, Y. / Terasawa, H. / Akira, S. / Fujita, T. / Inagaki, F.
History
DepositionJan 4, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)56,7582
Polymers56,7582
Non-polymers00
Water2,882160
1
A: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)28,3791
Polymers28,3791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)28,3791
Polymers28,3791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.808, 134.808, 69.340
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: 28379.062 Da / Num. of mol.: 2 / Fragment: residues 170-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPRO EX / Production host: Escherichia coli (E. coli) / References: UniProt: Q14653
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.02 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: magnesium formate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris1droppH7.9
3500 mM1dropNaCl
4100 mMsodium acetate1reservoirpH5.1
5400 mMmagnesium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: Jun 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.999→62.017 Å / Num. all: 42825 / Num. obs: 40856 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.999→2.11 Å / % possible all: 95.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 24036 / % possible obs: 94.6 % / Rmerge(I) obs: 0.094

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→62.017 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2419 1197 RANDOM
Rwork0.217 --
all0.2194 28981 -
obs0.2194 26977 -
Refinement stepCycle: LAST / Resolution: 2.3→62.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 0 160 3728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006636
X-RAY DIFFRACTIONc_angle_d1.2586
Refinement
*PLUS
Lowest resolution: 500 Å / % reflection Rfree: 9.2 % / Rfactor Rfree: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.26

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