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- PDB-6i3r: Structure, dynamics and roX2-lncRNA binding of tandem double-stra... -

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Basic information

Entry
Database: PDB / ID: 6i3r
TitleStructure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1/2 of Drosophila helicase MLE
ComponentsDosage compensation regulator
KeywordsRNA BINDING PROTEIN / Helicase / dsRBD
Function / homology
Function and homology information


RIP-mediated NFkB activation via ZBP1 / X chromosome located dosage compensation complex, transcription activating / dosage compensation complex assembly / 3'-5' DNA/RNA helicase activity / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / male courtship behavior, veined wing generated song production / regulation of cytoplasmic translation / regulatory region RNA binding / PKR-mediated signaling / MSL complex ...RIP-mediated NFkB activation via ZBP1 / X chromosome located dosage compensation complex, transcription activating / dosage compensation complex assembly / 3'-5' DNA/RNA helicase activity / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / male courtship behavior, veined wing generated song production / regulation of cytoplasmic translation / regulatory region RNA binding / PKR-mediated signaling / MSL complex / dosage compensation by hyperactivation of X chromosome / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / sex-chromosome dosage compensation / polytene chromosome / 3'-5' RNA helicase activity / regulation of mRNA processing / axon extension / lncRNA binding / DNA duplex unwinding / nuclear chromosome / positive regulation of heterochromatin formation / X chromosome / 3'-5' DNA helicase activity / DNA helicase activity / helicase activity / determination of adult lifespan / double-stranded RNA binding / chromosome / double-stranded DNA binding / RNA helicase activity / RNA helicase / ribonucleoprotein complex / chromatin binding / chromatin / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / RNA binding / ATP binding / nucleus / cytosol
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 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 / 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
Dosage compensation regulator mle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsJagtap, P.K.A. / Buelow, S.v. / Masiewicz, P. / Simon, B. / Hennig, J.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless.
Authors: Ankush Jagtap, P.K. / Muller, M. / Masiewicz, P. / von Bulow, S. / Hollmann, N.M. / Chen, P.C. / Simon, B. / Thomae, A.W. / Becker, P.B. / Hennig, J.
History
DepositionNov 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_related
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
Revision 1.5Jun 19, 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: Dosage compensation regulator


Theoretical massNumber of molelcules
Total (without water)28,5901
Polymers28,5901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21270 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Dosage compensation regulator / ATP-dependent RNA helicase mle / Protein male-less / Protein maleless / Protein no action potential


Mass: 28589.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: mle, nap, CG11680 / Production host: Escherichia coli (E. coli) / References: UniProt: P24785, RNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic33D (H)CCH-TOCSY
131isotropic33D HN(CA)CB
141isotropic33D HNCA
151isotropic33D CBCA(CO)NH
161isotropic13D 1H-13C NOESY aliphatic
171isotropic13D H(CCO)NH
181isotropic13D HNCO
191isotropic13D HBHA(CO)NH
1101isotropic13D 1H-15N NOESY
1111isotropic32D 1H-13C HSQC aromatic
1121isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] MLE dsRBD1,2, 90% H2O/10% D2O
Label: 13C, 15N labelled / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: MLE dsRBD1,2 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 20mM NaPi ph 6.5, 200mM NaCl, 1mM DTT / Ionic strength: 200 mM / Label: NMR Buffer / pH: 6 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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