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- PDB-2irf: CRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX. -

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Basic information

Entry
Database: PDB / ID: 2irf
TitleCRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX.
Components
  • DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')
  • DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')
  • INTERFERON REGULATORY FACTOR 2Interferon regulatory factors
KeywordsGENE REGULATION/DNA / TRANSCRIPTION FACTOR / IFN INDUCTION / IRF FAMILY / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


toll-like receptor 3 signaling pathway / immune system process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / focal adhesion ...toll-like receptor 3 signaling pathway / immune system process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / focal adhesion / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
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 / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / 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 / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / 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 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsFujii, Y. / Shimizu, T. / Kusumoto, M. / Kyogoku, Y. / Taniguchi, T. / Hakoshima, T.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences.
Authors: Fujii, Y. / Shimizu, T. / Kusumoto, M. / Kyogoku, Y. / Taniguchi, T. / Hakoshima, T.
History
DepositionMay 30, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')
B: DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')
C: DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')
D: DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')
E: DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')
F: DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')
G: INTERFERON REGULATORY FACTOR 2
H: INTERFERON REGULATORY FACTOR 2
I: INTERFERON REGULATORY FACTOR 2
J: INTERFERON REGULATORY FACTOR 2
K: INTERFERON REGULATORY FACTOR 2
L: INTERFERON REGULATORY FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,70118
Polymers104,46712
Non-polymers2356
Water7,152397
1
A: DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')
F: DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')
G: INTERFERON REGULATORY FACTOR 2
H: INTERFERON REGULATORY FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9006
Polymers34,8224
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')
E: DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')
I: INTERFERON REGULATORY FACTOR 2
J: INTERFERON REGULATORY FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9006
Polymers34,8224
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')
D: DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')
K: INTERFERON REGULATORY FACTOR 2
L: INTERFERON REGULATORY FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9006
Polymers34,8224
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.300, 132.300, 296.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522

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Components

#1: DNA chain DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')


Mass: 3871.362 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')


Mass: 3979.403 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Protein
INTERFERON REGULATORY FACTOR 2 / Interferon regulatory factors / IRF-2


Mass: 13485.710 Da / Num. of mol.: 6 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: T7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23906
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.8
Details: 50 MM MES-K (PH 5.8), 50 MM KCL, 4% 2-MPD,, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2KCL11
3MPD11
4MES12
5KCL12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMMes-K1reservoir
250 mM1reservoirKCl
34 %1reservoir
4protein1drop
513mer DNA1drop
61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 35660 / % possible obs: 88.4 % / Observed criterion σ(I): 1 / Redundancy: 35.8 % / Biso Wilson estimate: 22.26 Å2 / Rsym value: 0.062
Reflection shellResolution: 2.1→2.2 Å / % possible all: 76.1
Reflection
*PLUS
Num. obs: 69536 / Num. measured all: 2494554 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 77.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.243 8 5 %
Rwork0.202 --
obs0.202 35660 88.4 %
Displacement parametersBiso mean: 26.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 1504 12 397 7397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
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
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.308 8 4.6 %
Rwork0.261 --
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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