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- PDB-1whq: Solution structure of the N-terminal dsRBD from hypothetical prot... -

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Basic information

Entry
Database: PDB / ID: 1whq
TitleSolution structure of the N-terminal dsRBD from hypothetical protein BAB28848
ComponentsRNA helicase A
KeywordsRNA BINDING PROTEIN / double-stranded RNA binding domain / dsRBD / DSRM / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


catalytic activity, acting on a nucleic acid / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulatory region RNA binding / mRNA Splicing - Major Pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / regulation of cytoplasmic translation / positive regulation of RNA export from nucleus / PKR-mediated signaling ...catalytic activity, acting on a nucleic acid / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulatory region RNA binding / mRNA Splicing - Major Pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / regulation of cytoplasmic translation / positive regulation of RNA export from nucleus / PKR-mediated signaling / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / triplex DNA binding / RISC complex binding / CRD-mediated mRNA stabilization / nucleoside triphosphate diphosphatase activity / importin-alpha family protein binding / perichromatin fibrils / positive regulation of interleukin-18 production / nuclear stress granule / 3'-5' RNA helicase activity / alternative mRNA splicing, via spliceosome / miRNA-mediated post-transcriptional gene silencing / RISC-loading complex / regulation of mRNA processing / regulation of defense response to virus by host / RISC complex assembly / positive regulation of response to cytokine stimulus / positive regulation of cytoplasmic translation / positive regulation of innate immune response / RISC complex / sequence-specific mRNA binding / RNA polymerase binding / 3'-5' DNA helicase activity / cellular response to exogenous dsRNA / pyroptotic inflammatory response / positive regulation of interferon-alpha production / DNA replication origin binding / mRNA transport / DNA helicase activity / positive regulation of interferon-beta production / positive regulation of DNA repair / ribonucleoside triphosphate phosphatase activity / positive regulation of DNA replication / promoter-specific chromatin binding / DNA-templated transcription termination / chromatin DNA binding / positive regulation of interleukin-6 production / cytoplasmic ribonucleoprotein granule / RNA stem-loop binding / circadian rhythm / positive regulation of inflammatory response / positive regulation of fibroblast proliferation / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / actin cytoskeleton / single-stranded DNA binding / double-stranded RNA binding / chromatin organization / cellular response to heat / double-stranded DNA binding / single-stranded 3'-5' DNA helicase activity / transcription coactivator activity / single-stranded RNA binding / RNA helicase activity / nuclear body / RNA helicase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ribonucleoprotein complex / innate immune response / mRNA binding / centrosome / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / metal ion binding / 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 (HA2), winged-helix / Helicase-associated domain / 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 (HA2), winged-helix / Helicase-associated domain / 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 domain / DEAD/DEAH box helicase / 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. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the N-terminal dsRBD from hypothetical protein BAB28848
Authors: Nagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA helicase A


Theoretical massNumber of molelcules
Total (without water)10,7331
Polymers10,7331
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
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA helicase A


Mass: 10733.122 Da / Num. of mol.: 1 / Fragment: double-stranded RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: RIKEN cDNA 2810480H04 / Plasmid: P021209-25 / 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: 1.16mM PROTEIN U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6 / 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
NMRView5.0.4Johnsondata analysis
CYANA2Guentertstructure solution
NMRPipe2.3Delaglioprocessing
KUJIRA0.901Kobayashi, N.data analysis
CYANA2Guentertrefinement
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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