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- PDB-1irg: INTERFERON REGULATORY FACTOR-2 DNA BINDING DOMAIN, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1irg
TitleINTERFERON REGULATORY FACTOR-2 DNA BINDING DOMAIN, NMR, 20 STRUCTURES
ComponentsINTERFERON REGULATORY FACTOR-2Interferon regulatory factors
KeywordsTRANSCRIPTION REGULATION / WINGED HELIX-TURN-HELIX
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
Interferon regulatory factor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsFurui, J. / Uegaki, K. / Yamazaki, T. / Shirakawa, M. / Swindells, M.B. / Harada, H. / Taniguchi, T. / Kyogoku, Y.
Citation
Journal: Structure / Year: 1998
Title: Solution structure of the IRF-2 DNA-binding domain: a novel subgroup of the winged helix-turn-helix family.
Authors: Furui, J. / Uegaki, K. / Yamazaki, T. / Shirakawa, M. / Swindells, M.B. / Harada, H. / Taniguchi, T. / Kyogoku, Y.
#1: Journal: FEBS Lett. / Year: 1995
Title: Secondary Structure and Folding Topology of the DNA Binding Domain of Interferon Regulatory Factor 2, as Revealed by NMR Spectroscopy
Authors: Uegaki, K. / Shirakawa, M. / Harada, H. / Taniguchi, T. / Kyogoku, Y.
History
DepositionNov 25, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERFERON REGULATORY FACTOR-2


Theoretical massNumber of molelcules
Total (without water)13,3551
Polymers13,3551
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100THE LOWEST TARGET FUNCTIONS
Representative

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Components

#1: Protein INTERFERON REGULATORY FACTOR-2 / Interferon regulatory factors


Mass: 13354.515 Da / Num. of mol.: 1 / Fragment: RESIDUES 2 - 113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Cellular location: NUCLEUSCell nucleus / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (LAMBDA DE3) / References: UniProt: P23906

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED 3D NOESY
12113C -EDITED 3D NOESY
1312D NOESY

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Sample preparation

Sample conditionspH: 5.70 / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
JEOL ARX500JEOLARX5006002
JEOL ALPHA600JEOLALPHA6006003

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURAL STATISTICS: AVERAGE SD RMSD FROM EXPERIMENTAL DISTANCE RESTRAINTS ALL (1453) 0.025 A 0.001 A INTRARESIDUE NOE (415) 0.022 A 0.001 A SEQUENTIAL NOE (|I-J|=1) (381) 0.025 A 0.003 A MEDIUM RANGE NOE (1<|I-J|<5) (242) 0.026 A 0.004 A LONG RANGE NOE (|I-J|>=5) (363) 0.022 A 0.003 A HYDROGEN BOND (52)* 0.051 A 0.002 A
NMR ensembleConformer selection criteria: THE LOWEST TARGET FUNCTIONS / Conformers calculated total number: 100 / Conformers submitted total number: 20

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