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- PDB-2dix: Solution structure of the DSRM domain of Protein activator of the... -

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Basic information

Entry
Database: PDB / ID: 2dix
TitleSolution structure of the DSRM domain of Protein activator of the interferon-induced protein kinase
ComponentsInterferon-inducible double stranded RNA-dependent protein kinase activator A
KeywordsRNA BINDING PROTEIN / structure genomics / DSRM domain / Hypothetical protein PRKRA / 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 regulatory ncRNA processing / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / RISC-loading complex / RISC complex assembly / miRNA processing / pre-miRNA processing / siRNA processing / siRNA binding / RISC complex ...regulation of regulatory ncRNA processing / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / RISC-loading complex / RISC complex assembly / miRNA processing / pre-miRNA processing / siRNA processing / siRNA binding / RISC complex / outer ear morphogenesis / middle ear morphogenesis / skeletal system morphogenesis / MicroRNA (miRNA) biogenesis / enzyme activator activity / positive regulation of intrinsic apoptotic signaling pathway / response to virus / PKR-mediated signaling / double-stranded RNA binding / cellular response to oxidative stress / protein stabilization / immune response / negative regulation of cell population proliferation / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
PRKRA, first double-stranded RNA binding domain / PRKRA, second double-stranded RNA binding domain / PRKRA, third 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Interferon-inducible double-stranded RNA-dependent protein kinase activator A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDang, W. / 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 DSRM domain of Protein activator of the interferon-induced protein kinase
Authors: Dang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S.
History
DepositionMar 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 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_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
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-inducible double stranded RNA-dependent protein kinase activator A


Theoretical massNumber of molelcules
Total (without water)8,8461
Polymers8,8461
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, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Interferon-inducible double stranded RNA-dependent protein kinase activator A / Protein activator of the interferon-induced protein kinase / Protein kinase / interferon-inducible ...Protein activator of the interferon-induced protein kinase / Protein kinase / interferon-inducible double stranded RNA dependent activator / PKR-associated protein X / Hypothetical protein DKFZp564I0123


Mass: 8845.986 Da / Num. of mol.: 1 / Fragment: DSRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell free protein synthesis / Gene: PRKRA, DKFZp564I0123, PACT / Plasmid: P050912-05 / Production host: Cell free synthesis / References: UniProt: O75569

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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: 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / 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
KUJIRA0.9321Kobayashi, 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, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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