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- PDB-1if1: INTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA -

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Basic information

Entry
Database: PDB / ID: 1if1
TitleINTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA
Components
  • DNA (26-MER)
  • PROTEIN (INTERFERON REGULATORY FACTOR 1)
KeywordsTRANSCRIPTION/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / TRANSCRIPTION FACTOR / INTERFERON REGULATION / HELIX-TURN-HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


CD8-positive, alpha-beta T cell differentiation / regulation of MyD88-dependent toll-like receptor signaling pathway / positive regulation of natural killer cell differentiation / regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of T-helper 1 cell differentiation / regulation of adaptive immune response / negative regulation of regulatory T cell differentiation / toll-like receptor 3 signaling pathway / negative regulation of T-helper 2 cell differentiation / regulation of innate immune response ...CD8-positive, alpha-beta T cell differentiation / regulation of MyD88-dependent toll-like receptor signaling pathway / positive regulation of natural killer cell differentiation / regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of T-helper 1 cell differentiation / regulation of adaptive immune response / negative regulation of regulatory T cell differentiation / toll-like receptor 3 signaling pathway / negative regulation of T-helper 2 cell differentiation / regulation of innate immune response / type II interferon-mediated signaling pathway / positive regulation of type I interferon production / cellular response to interferon-beta / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / cellular response to mechanical stimulus / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Interferon regulatory factor-1/2 / 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. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Interferon regulatory factor-1/2 / 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. / 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 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsEscalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A.
Citation
Journal: Nature / Year: 1998
Title: Structure of IRF-1 with bound DNA reveals determinants of interferon regulation.
Authors: Escalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A.K.
#1: Journal: FEBS Lett. / Year: 1997
Title: Expression, Purification, and Co-Crystallization of Irf-1 Bound to the Interferon-Beta Element Prdi
Authors: Escalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A.K.
History
DepositionSep 12, 1997Processing site: NDB
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Feb 7, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (26-MER)
D: DNA (26-MER)
A: PROTEIN (INTERFERON REGULATORY FACTOR 1)
B: PROTEIN (INTERFERON REGULATORY FACTOR 1)


Theoretical massNumber of molelcules
Total (without water)42,8124
Polymers42,8124
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.800, 84.800, 203.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.823802, 0.55224, -0.127987), (0.566506, 0.79384, -0.221107), (-0.020503, -0.254654, -0.966815)
Vector: 106.722, -28.833, 29.2859)

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Components

#1: DNA chain DNA (26-MER)


Mass: 7986.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein PROTEIN (INTERFERON REGULATORY FACTOR 1)


Mass: 13419.605 Da / Num. of mol.: 2 / Fragment: DNA-BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: MOUSE FIBROBLAST L929 / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P15314
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 18-22% PEG8K, 300 MM AMMONIUM ACETATE (PH 6.5), 10% GLYCEROL.
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / Details: Escalante, C.R., (1997) FEBS Lett., 414, 219.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 %PEG800011
2300 mMammonium acetate11

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 1, 1996 / Details: DUAL SLITS
RadiationMonochromator: SILICON CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 20328 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 15.3
Reflection shellResolution: 3→3.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 13.5 / Rsym value: 0.09 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. obs: 21657 / % possible obs: 99.1 % / Num. measured all: 125805
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.23 Å / % possible obs: 99.7 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3→12 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.309 -10 %RANDOM
Rwork0.242 ---
obs0.242 20328 --
Displacement parametersBiso mean: 29.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.642 Å20 Å2
2--0.642 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 1054 0 10 2779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINTS30.066300300
2230.08300300
3350.0741010
4450.0591010
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMODDNA-RNA.TOPMOD
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.97 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg2.3

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