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- PDB-2pi0: Crystal Structure of IRF-3 bound to the PRDIII-I regulatory eleme... -

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Basic information

Entry
Database: PDB / ID: 2pi0
TitleCrystal Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-B enhancer
Components
  • Interferon regulatory factor 3IRF3
  • PRDIII-I region of human interferon-B promoter strand 1
  • PRDIII-I region of human interferon-B promoter strand 2
Keywordstranscription activator/DNA / Interferon / Protein-DNA complex / Transcription / transcription activator-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 / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / mRNA transcription / toll-like receptor 4 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 / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / mRNA transcription / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / DNA-binding transcription activator activity / immune system process / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / positive regulation of type I interferon 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 / 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 / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / 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 / 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 / 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 / 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: 2.31 Å
AuthorsEscalante, C.R. / Nistal-Villan, E. / Leyi, S. / Garcia-Sastre, A. / Aggarwal, A.K.
CitationJournal: Mol.Cell / Year: 2007
Title: Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-beta enhancer.
Authors: Escalante, C.R. / Nistal-Villan, E. / Shen, L. / Garcia-Sastre, A. / Aggarwal, A.K.
History
DepositionApr 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_special_symmetry / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PRDIII-I region of human interferon-B promoter strand 1
F: PRDIII-I region of human interferon-B promoter strand 2
A: Interferon regulatory factor 3
B: Interferon regulatory factor 3
C: Interferon regulatory factor 3
D: Interferon regulatory factor 3


Theoretical massNumber of molelcules
Total (without water)73,2726
Polymers73,2726
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.417, 46.132, 129.325
Angle α, β, γ (deg.)90.00, 129.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-123-

HOH

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Components

#1: DNA chain PRDIII-I region of human interferon-B promoter strand 1


Mass: 10069.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: DNA chain PRDIII-I region of human interferon-B promoter strand 2


Mass: 9610.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#3: Protein
Interferon regulatory factor 3 / IRF3 / IRF-3


Mass: 13398.122 Da / Num. of mol.: 4 / Fragment: IRF-3 DNA Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Plasmid: PET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q14653
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12%PEG 400,200mM NaCl, pH 7., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2NaClSodium chloride11
3PEG 40012
4NaClSodium chloride12

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Data collection

DiffractionMean temperature: 109 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 30304 / % possible obs: 91.7 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.027 / Rsym value: 0.027 / Net I/σ(I): 34.8
Reflection shellHighest resolution: 2.31 Å / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 10.8 / Rsym value: 0.055 / % possible all: 74.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T2K

1t2k


Resolution: 2.31→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.449 / SU ML: 0.17 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26433 1530 5 %RANDOM
Rwork0.18101 ---
obs0.18519 28772 86.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å2-3.39 Å2
2--3.33 Å20 Å2
3----4.84 Å2
Refinement stepCycle: LAST / Resolution: 2.31→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 1306 0 123 4790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0214930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4482.286972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5095415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31822.189169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.23415527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3171538
X-RAY DIFFRACTIONr_chiral_restr0.1270.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023407
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.22004
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23088
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5591.52167
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.56323353
X-RAY DIFFRACTIONr_scbond_it4.06733666
X-RAY DIFFRACTIONr_scangle_it5.6874.53619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 28 -
Rwork0.193 440 -
obs--18.4 %
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)
13.364-0.87670.11822.4387-0.85393.60060.12290.1744-0.1943-0.2275-0.0299-0.23780.54130.3401-0.0930.00070.08180.0496-0.1154-0.058-0.028233.2734-15.35673.0781
22.59390.0716-0.05881.3130.31540.94090.09240.1674-0.0624-0.0249-0.03890.0331-0.0926-0.0549-0.0535-0.03020.0359-0.0317-0.0619-0.0047-0.02537.12487.249217.5611
33.09250.23780.93581.06950.13511.43080.13720.1914-0.08530.0036-0.0887-0.0034-0.03320.1722-0.0485-0.08430.0288-0.02410.02150.0085-0.044338.91353.9937.9026
41.86620.4243-0.41771.7191-0.70722.7390.03610.015-0.11530.0267-0.0216-0.03-0.0894-0.0839-0.0145-0.05320.0030.0135-0.079-0.0201-0.016313.2942-2.026862.1075
50.08570.1076-0.04460.3440.09081.7040.1060.0181-0.0086-0.02870.0627-0.01-0.10370.0672-0.1687-0.0090.0137-0.0048-0.0049-0.0345-0.022222.34253.298129.1859
60.00960.0492-0.00330.2534-0.01720.00120.0258-0.0354-0.0311-0.0357-0.0262-0.01220.02110.01050.0004-0.00980.0272-0.00450.0016-0.02460.004421.61990.101131.8958
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC5 - 438 - 46
2X-RAY DIFFRACTION1AC52 - 11055 - 113
3X-RAY DIFFRACTION2BD1 - 1124 - 115
4X-RAY DIFFRACTION3CE4 - 1107 - 113
5X-RAY DIFFRACTION4DF3 - 466 - 49
6X-RAY DIFFRACTION4DF52 - 11155 - 114
7X-RAY DIFFRACTION5EA2 - 331 - 32
8X-RAY DIFFRACTION5FB2 - 331 - 32
9X-RAY DIFFRACTION6AG114 - 1291 - 16
10X-RAY DIFFRACTION6BH114 - 1361 - 23
11X-RAY DIFFRACTION6CI114 - 1341 - 21
12X-RAY DIFFRACTION6DJ114 - 1391 - 26
13X-RAY DIFFRACTION6EK35 - 491 - 15
14X-RAY DIFFRACTION6FL34 - 521 - 19

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