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- PDB-3qu6: Crystal structure of IRF-3 DBD free form -

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Basic information

Entry
Database: PDB / ID: 3qu6
TitleCrystal structure of IRF-3 DBD free form
ComponentsIRF3 protein
KeywordsDNA BINDING PROTEIN / Helix-turn-helix / Gene regulation
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 / mRNA transcription / TRAF6 mediated IRF7 activation ...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 / mRNA transcription / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / positive regulation of cytokine production involved in inflammatory response / type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / DNA-binding transcription activator activity / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / positive regulation of interferon-alpha production / immune system process / positive regulation of type I interferon production / positive regulation of interferon-beta production / TICAM1-dependent activation of IRF3/IRF7 / Regulation of innate immune responses to cytosolic DNA / antiviral innate immune response / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / cellular response to virus / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / DNA-binding transcription repressor activity, RNA polymerase II-specific / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / 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 / defense response to virus / sequence-specific DNA binding / regulation of apoptotic process / 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 / apoptotic process / regulation of transcription by RNA polymerase II / DNA damage response / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / DNA binding / DNA-templated transcription / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / 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 / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / 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
Interferon regulatory factor 3 / Interferon regulatory factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDe Ioannes, P.E. / Escalante, C.R. / Aggarwal, A.K.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structures of apo IRF-3 and IRF-7 DNA binding domains: effect of loop L1 on DNA binding.
Authors: De Ioannes, P. / Escalante, C.R. / Aggarwal, A.K.
History
DepositionFeb 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: IRF3 protein
B: IRF3 protein
C: IRF3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,15422
Polymers40,2483
Non-polymers90619
Water2,720151
1
A: IRF3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,86611
Polymers13,4161
Non-polymers44910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IRF3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6055
Polymers13,4161
Non-polymers1894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: IRF3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6836
Polymers13,4161
Non-polymers2675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.908, 64.908, 157.621
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
11C-140-

HOH

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Components

#1: Protein IRF3 protein


Mass: 13416.160 Da / Num. of mol.: 3 / Fragment: DNA Binding Domain / Mutation: L84M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: Pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLyS / References: UniProt: Q7Z5G6, UniProt: Q14653*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% PEG 1K, 100 mM NaAc, 300 mM ZnCl2, 8% cadaverine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 3, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→38.384 Å / Num. all: 25580 / Num. obs: 25580 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 27.6

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Processing

Software
NameVersionClassification
JDirectordata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PI0

2pi0


Resolution: 2.3→38.384 Å / SU ML: 0.31 / Isotropic thermal model: 23 / σ(F): 1.35 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 892 5.09 %
Rwork0.2132 --
obs0.2157 17521 98.4 %
all-17524 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.471 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5341 Å20 Å20 Å2
2---0.5341 Å2-0 Å2
3---1.0681 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 19 151 2539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092479
X-RAY DIFFRACTIONf_angle_d1.1923362
X-RAY DIFFRACTIONf_dihedral_angle_d15.846891
X-RAY DIFFRACTIONf_chiral_restr0.096335
X-RAY DIFFRACTIONf_plane_restr0.007437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44420.33571350.26312757X-RAY DIFFRACTION100
2.4442-2.63290.33621560.26972746X-RAY DIFFRACTION99
2.6329-2.89780.36851600.24092731X-RAY DIFFRACTION99
2.8978-3.31690.25391590.23292754X-RAY DIFFRACTION99
3.3169-4.17810.2231490.18722749X-RAY DIFFRACTION97
4.1781-38.38940.22331330.19112892X-RAY DIFFRACTION96

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