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- PDB-1uil: Double-stranded RNA-binding motif of Hypothetical protein BAB28848 -

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Basic information

Entry
Database: PDB / ID: 1uil
TitleDouble-stranded RNA-binding motif of Hypothetical protein BAB28848
ComponentsDouble-stranded RNA-binding motif
KeywordsRNA BINDING PROTEIN / Structural genomics / Double-stranded RNA-binding motif / DSRM / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


single-stranded 3'-5' DNA helicase activity / positive regulation of viral translation / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / regulatory region RNA binding / RIP-mediated NFkB activation via ZBP1 / : / mRNA Splicing - Major Pathway ...single-stranded 3'-5' DNA helicase activity / positive regulation of viral translation / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / regulatory region RNA binding / RIP-mediated NFkB activation via ZBP1 / : / mRNA Splicing - Major Pathway / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription / PKR-mediated signaling / RISC complex binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / triplex DNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / G-quadruplex DNA unwinding / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / nucleoside triphosphate diphosphatase activity / nuclear stress granule / 3'-5' RNA helicase activity / perichromatin fibrils / positive regulation of interleukin-18 production / RNA secondary structure unwinding / RISC-loading complex / regulation of mRNA processing / miRNA-mediated post-transcriptional gene silencing / RISC complex assembly / positive regulation of response to cytokine stimulus / regulation of defense response to virus by host / positive regulation of cytoplasmic translation / importin-alpha family protein binding / siRNA binding / alternative mRNA splicing, via spliceosome / RNA stem-loop binding / positive regulation of innate immune response / RISC complex / sequence-specific mRNA binding / RNA polymerase binding / 3'-5' DNA helicase activity / DNA duplex unwinding / cellular response to exogenous dsRNA / RNA polymerase II complex binding / DNA replication origin binding / pyroptosis / positive regulation of interferon-alpha production / mRNA transport / positive regulation of DNA replication / : / positive regulation of DNA repair / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / promoter-specific chromatin binding / DNA-templated transcription termination / : / transcription coregulator activity / chromatin DNA binding / cytoplasmic ribonucleoprotein granule / positive regulation of inflammatory response / positive regulation of interleukin-6 production / circadian rhythm / positive regulation of fibroblast proliferation / actin cytoskeleton / positive regulation of tumor necrosis factor production / double-stranded RNA binding / single-stranded DNA binding / cellular response to heat / positive regulation of NF-kappaB transcription factor activity / cellular response to tumor necrosis factor / double-stranded DNA binding / protein-containing complex assembly / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / single-stranded RNA binding / transcription coactivator activity / nuclear body / RNA helicase / inflammatory response / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / mRNA binding / centrosome / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsNagata, T. / Muto, Y. / Hayashi, F. / Hamana, H. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. ...Nagata, T. / Muto, Y. / Hayashi, F. / Hamana, H. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Hayashizaki, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of Double-stranded RNA-binding motif of Hypothetical protein BAB28848
Authors: Nagata, T. / Muto, Y. / Hayashi, F. / Hamana, H. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, ...Authors: Nagata, T. / Muto, Y. / Hayashi, F. / Hamana, H. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Hayashizaki, Y. / Yokoyama, S.
History
DepositionJul 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Double-stranded RNA-binding motif


Theoretical massNumber of molelcules
Total (without water)12,5071
Polymers12,5071
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
RepresentativeModel #1lowest energy

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Components

#1: Protein Double-stranded RNA-binding motif / Hypothetical protein BAB28848


Mass: 12506.934 Da / Num. of mol.: 1 / Fragment: residues 1-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RIKEN cDNA 2810480H04 / Plasmid: P021209-28 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: O70133

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.3mM PROTEIN U-15N, 13C; 20mM Phosphate buffer Na; 100mM NaCl; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
KUJIRA0.816Kobayashi, N.data analysis
NMRView5.0.4Johnsondata analysis
NMRPipe1.8Delaglioprocessing
CYANA1Guentertstructure solution
CYANA1Guentertrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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