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- PDB-1x49: Solution structure of the first DSRM domain in Interferon-induced... -

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Entry
Database: PDB / ID: 1x49
TitleSolution structure of the first DSRM domain in Interferon-induced, double-stranded RNA-activated protein kinase
ComponentsInterferon-induced, double-stranded RNA-activated protein kinase
KeywordsRNA BINDING PROTEIN / structure genomics / DSRM domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / ISG15 antiviral mechanism / eukaryotic translation initiation factor 2alpha kinase activity / PKR-mediated signaling / response to interferon-alpha / positive regulation of stress-activated MAPK cascade / regulation of hematopoietic progenitor cell differentiation / negative regulation of osteoblast proliferation / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation ...regulation of NLRP3 inflammasome complex assembly / ISG15 antiviral mechanism / eukaryotic translation initiation factor 2alpha kinase activity / PKR-mediated signaling / response to interferon-alpha / positive regulation of stress-activated MAPK cascade / regulation of hematopoietic progenitor cell differentiation / negative regulation of osteoblast proliferation / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / negative regulation of viral genome replication / antiviral innate immune response / response to vitamin E / endoplasmic reticulum unfolded protein response / positive regulation of chemokine production / cellular response to amino acid starvation / positive regulation of cytokine production / non-specific protein-tyrosine kinase / response to virus / non-membrane spanning protein tyrosine kinase activity / response to toxic substance / positive regulation of non-canonical NF-kappaB signal transduction / double-stranded RNA binding / positive regulation of NF-kappaB transcription factor activity / kinase activity / response to lipopolysaccharide / positive regulation of MAPK cascade / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / translation / positive regulation of apoptotic process / protein serine kinase activity / negative regulation of apoptotic process / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHe, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the first DSRM domain in Interferon-induced, double-stranded RNA-activated protein kinase
Authors: He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S.
History
DepositionMay 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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-induced, double-stranded RNA-activated protein kinase


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water0
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
RepresentativeModel #1lowest energy

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Components

#1: Protein Interferon-induced, double-stranded RNA-activated protein kinase / Interferon-inducible RNA-dependent protein kinase / p68 kinase / P1/eIF-2A protein kinase / ...Interferon-inducible RNA-dependent protein kinase / p68 kinase / P1/eIF-2A protein kinase / Serine/threonine-protein kinase TIK


Mass: 10580.726 Da / Num. of mol.: 1 / Fragment: DSRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell free protein synthesis / Gene: Prkr, Eif2ak2, Pkr, Tik / Plasmid: P040712-15
References: UniProt: Q03963, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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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: 0.8mM U-15,13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.863Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,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
Conformers calculated total number: 100 / Conformers submitted total number: 20

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