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- PDB-2rs7: Solution structure of the second dsRBD from RNA helicase A -

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Basic information

Entry
Database: PDB / ID: 2rs7
TitleSolution structure of the second dsRBD from RNA helicase A
ComponentsATP-dependent RNA helicase A
KeywordsHYDROLASE / double-stranded RNA binding domain / dsRBD / dsrm / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


single-stranded 3'-5' DNA helicase activity / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / 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 / positive regulation of RNA export from nucleus / PKR-mediated signaling ...single-stranded 3'-5' DNA helicase activity / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / 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 / positive regulation of RNA export from nucleus / PKR-mediated signaling / triplex DNA binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / RISC complex binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / G-quadruplex DNA unwinding / nucleoside triphosphate diphosphatase activity / nuclear stress granule / positive regulation of interleukin-18 production / perichromatin fibrils / 3'-5' RNA helicase activity / alternative mRNA splicing, via spliceosome / RNA secondary structure unwinding / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / RISC complex assembly / regulation of mRNA processing / regulation of defense response to virus by host / importin-alpha family protein binding / 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 / DNA duplex unwinding / 3'-5' DNA helicase activity / cellular response to exogenous dsRNA / pyroptotic inflammatory response / DNA replication origin binding / positive regulation of interferon-alpha production / mRNA transport / positive regulation of interferon-beta production / DNA helicase activity / 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 inflammatory response / cytoplasmic ribonucleoprotein granule / circadian rhythm / positive regulation of interleukin-6 production / RNA stem-loop binding / positive regulation of tumor necrosis factor production / double-stranded RNA binding / positive regulation of fibroblast proliferation / actin cytoskeleton / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / single-stranded DNA binding / cellular response to heat / double-stranded DNA binding / RNA helicase activity / transcription coactivator activity / single-stranded RNA binding / nuclear body / RNA helicase / ribonucleoprotein complex / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / 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 / simulated annealing, torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsNagata, T. / Muto, Y. / Tsuda, K. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2012
Title: Solution structures of the double-stranded RNA-binding domains from RNA helicase A
Authors: Nagata, T. / Tsuda, K. / Kobayashi, N. / Shirouzu, M. / Kigawa, T. / Guntert, P. / Yokoyama, S. / Muto, Y.
History
DepositionNov 29, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase A


Theoretical massNumber of molelcules
Total (without water)12,5071
Polymers12,5071
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein ATP-dependent RNA helicase A / DEAH box protein 9 / mHEL-5 / Nuclear DNA helicase II / NDH II


Mass: 12506.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dhx9, Ddx9 / Production host: cell-free protein synthesis (unknown) / References: UniProt: O70133, RNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY

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Sample preparation

DetailsContents: 1.16 mM [U-100% 13C; U-100% 15N] entity-1, 20 mM sodium phosphate-2, 100 mM sodium chloride-3, 1 mM DTT-4, 0.02 % sodium azide-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.16 mMentity-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
1 mMDTT-41
0.02 %sodium azide-51
Sample conditionsIonic strength: 120 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
CYANArefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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