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- PDB-2dll: Solution structure of the IRF domain of human interferon regulato... -

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Basic information

Entry
Database: PDB / ID: 2dll
TitleSolution structure of the IRF domain of human interferon regulator factors 4
ComponentsInterferon regulatory factor 4
KeywordsCYTOKINE / IRF domain / Interferon regulatory factor 4 / Lymphocyte specific interferon regulatory factor / NF-EM5 / Multiple myeloma oncogene 1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / positive regulation of interleukin-13 production / defense response to protozoan / positive regulation of interleukin-4 production / immune system process / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of interleukin-10 production / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / positive regulation of interleukin-2 production ...T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / positive regulation of interleukin-13 production / defense response to protozoan / positive regulation of interleukin-4 production / immune system process / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of interleukin-10 production / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / positive regulation of interleukin-2 production / Nuclear events stimulated by ALK signaling in cancer / T cell activation / Interferon gamma signaling / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / nucleosome / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / 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 / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZhang, H.P. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the IRF domain of human interferon regulator factors 4
Authors: Zhang, H.P. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)13,9111
Polymers13,9111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Interferon regulatory factor 4 / IRF-4 / Lymphocyte-specific interferon regulatory factor / LSIRF / NF-EM5 / Multiple myeloma oncogene 1


Mass: 13910.570 Da / Num. of mol.: 1 / Fragment: IRF domain, residues 8-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: IRF4, MUM1 / Plasmid: P050516-06 / Production host: Cell free synthesis / References: UniProt: Q15306

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.23mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.04Johnson, B.A.data analysis
KUJIRA0.93191Kobayashi, N.data analysis
CYANA2.0.17Guntent, P.structure solution
CYANA2.0.17Guntent, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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