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- PDB-3qu3: Crystal structure of IRF-7 DBD apo form -

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Basic information

Entry
Database: PDB / ID: 3qu3
TitleCrystal structure of IRF-7 DBD apo form
ComponentsInterferon regulatory factor 7
KeywordsDNA BINDING PROTEIN / Helix-turn-helix / Gene regulation
Function / homology
Function and homology information


TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / regulation of MyD88-independent toll-like receptor signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / TRAF3-dependent IRF activation pathway / regulation of MyD88-dependent toll-like receptor signaling pathway / TRAF6 mediated IRF7 activation / regulation of adaptive immune response / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of type I interferon-mediated signaling pathway ...TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / regulation of MyD88-independent toll-like receptor signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / TRAF3-dependent IRF activation pathway / regulation of MyD88-dependent toll-like receptor signaling pathway / TRAF6 mediated IRF7 activation / regulation of adaptive immune response / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / regulation of innate immune response / positive regulation of interferon-alpha production / immunoglobulin mediated immune response / positive regulation of type I interferon production / cis-regulatory region sequence-specific DNA binding / positive regulation of interferon-beta production / regulation of gene expression / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / 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 / 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 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.3Feb 1, 2012Group: Refinement description
Revision 1.4Sep 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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: Interferon regulatory factor 7
B: Interferon regulatory factor 7
C: Interferon regulatory factor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,30210
Polymers46,9853
Non-polymers3177
Water5,170287
1
A: Interferon regulatory factor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6852
Polymers15,6621
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interferon regulatory factor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8715
Polymers15,6621
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Interferon regulatory factor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7473
Polymers15,6621
Non-polymers852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.588, 68.588, 68.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Interferon regulatory factor 7 / IRF-7


Mass: 15661.511 Da / Num. of mol.: 3 / Fragment: DNA Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Irf7 / Plasmid: Pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLyS / References: UniProt: P70434
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K
Details: 19% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.001
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2008 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL SAGITTAL FOCUSING MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.381
ReflectionResolution: 1.3→50 Å / Num. obs: 85736 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.3
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.4 / % possible all: 94.2

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Processing

Software
NameVersionClassification
CBASSdata 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 2O61

2o61


Resolution: 1.3→29.7 Å / σ(F): 2 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2 2027 2.37 %
Rwork0.161 --
obs0.169 85702 96.7 %
all-85702 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.1 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.3678 Å2-0 Å20 Å2
2---0.3678 Å2-0 Å2
3---0.7357 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 19 287 3191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083037
X-RAY DIFFRACTIONf_angle_d1.0294130
X-RAY DIFFRACTIONf_dihedral_angle_d13.4691110
X-RAY DIFFRACTIONf_chiral_restr0.066404
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33440.42061440.43975848X-RAY DIFFRACTION92
1.3344-1.37050.47321440.40965837X-RAY DIFFRACTION92
1.3705-1.41080.38321360.36365807X-RAY DIFFRACTION93
1.4108-1.45630.31611440.33115852X-RAY DIFFRACTION93
1.4563-1.50840.31981430.28765931X-RAY DIFFRACTION93
1.5084-1.56880.23891420.26875901X-RAY DIFFRACTION94
1.5688-1.64020.26411340.25865944X-RAY DIFFRACTION94
1.6402-1.72660.26521380.25995989X-RAY DIFFRACTION95
1.7266-1.83480.30681480.23685986X-RAY DIFFRACTION95
1.8348-1.97640.22441460.21826107X-RAY DIFFRACTION96
1.9764-2.17530.18711460.18646000X-RAY DIFFRACTION96
2.1753-2.48990.18951460.16746104X-RAY DIFFRACTION96
2.4899-3.13650.17931490.14146132X-RAY DIFFRACTION97
3.1365-29.70720.15971650.09226081X-RAY DIFFRACTION96

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