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- PDB-2n16: Solution structure of G-quadruplex recognition domain of RHAU -

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Basic information

Entry
Database: PDB / ID: 2n16
TitleSolution structure of G-quadruplex recognition domain of RHAU
ComponentsATP-dependent RNA helicase DHX36
KeywordsHYDROLASE
Function / homology
Function and homology information


positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / telomerase RNA stabilization / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / positive regulation of myeloid dendritic cell cytokine production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production ...positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / telomerase RNA stabilization / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / positive regulation of myeloid dendritic cell cytokine production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RNA secondary structure unwinding / G-quadruplex DNA binding / positive regulation of dendritic spine morphogenesis / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / regulation of transcription by RNA polymerase III / positive regulation of telomere maintenance / cellular response to arsenite ion / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to exogenous dsRNA / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / ATP-dependent activity, acting on DNA / positive regulation of interferon-alpha production / DNA helicase activity / regulation of mRNA stability / ossification / mRNA 3'-UTR binding / mRNA 5'-UTR binding / histone deacetylase binding / cytoplasmic stress granule / cellular response to UV / double-stranded RNA binding / single-stranded DNA binding / cellular response to heat / G-quadruplex RNA binding / spermatogenesis / perikaryon / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / DNA helicase / chromosome, telomeric region / RNA helicase activity / cell differentiation / negative regulation of translation / transcription cis-regulatory region binding / RNA helicase / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / innate immune response / dendrite / positive regulation of gene expression / magnesium ion binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase ...: / 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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
Similarity search - Domain/homology
ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsHeddi, B. / Cheong, V.V. / Martadinata, H. / Phan, A.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex.
Authors: Heddi, B. / Cheong, V.V. / Martadinata, H. / Phan, A.T.
History
DepositionMar 23, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references / Structure summary
Revision 1.2Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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 DHX36


Theoretical massNumber of molelcules
Total (without water)2,3611
Polymers2,3611
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ATP-dependent RNA helicase DHX36 / DEAH box protein 36 / G4-resolvase 1 / G4R1 / MLE-like protein 1 / RNA helicase associated with AU- ...DEAH box protein 36 / G4-resolvase 1 / G4R1 / MLE-like protein 1 / RNA helicase associated with AU-rich element ARE


Mass: 2360.802 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 53-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX36, DDX36, KIAA1488, MLEL1, RHAU / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2U1, DNA helicase, RNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1512D 1H-13C HSQC aliphatic
1613D C(CO)NH
1713D (H)CCH-TOCSY
1813D HNHA
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D H(CCO)NH

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Sample preparation

DetailsContents: 0.1-1 mM [U-100% 13C; U-100% 15N] entity-1, 10-70 mM potassium chloride-2, 10-20 mM potassium phosphate-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-100% 13C; U-100% 15N]0.1-11
mMpotassium chloride-210-701
mMpotassium phosphate-310-201
Sample conditionsIonic strength: 90 / pH: 6.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Braun and Wuthrichstructure solution
CYANAGuntert, Braun and Wuthrichrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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