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- PDB-2b7t: Structure of ADAR2 dsRBM1 -

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Basic information

Entry
Database: PDB / ID: 2b7t
TitleStructure of ADAR2 dsRBM1
ComponentsDouble-stranded RNA-specific editase 1
KeywordsHYDROLASE / RNA editing / RNA-binding protein
Function / homology
Function and homology information


C6 deamination of adenosine / Formation of editosomes by ADAR proteins / positive regulation of mRNA processing / hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / double-stranded RNA adenine deaminase / adenosine to inosine editing / tRNA-specific adenosine deaminase activity ...C6 deamination of adenosine / Formation of editosomes by ADAR proteins / positive regulation of mRNA processing / hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / double-stranded RNA adenine deaminase / adenosine to inosine editing / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / neuromuscular process controlling posture / neuromuscular synaptic transmission / innervation / mRNA modification / motor behavior / motor neuron apoptotic process / positive regulation of viral genome replication / RNA processing / negative regulation of cell migration / multicellular organism growth / mRNA processing / double-stranded RNA binding / regulation of cell cycle / negative regulation of cell population proliferation / synapse / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
ADAR2, first double-stranded RNA binding domain / ADAR2, second double-stranded RNA binding domain / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. ...ADAR2, first double-stranded RNA binding domain / ADAR2, second double-stranded RNA binding domain / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Double-stranded RNA-specific editase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsStefl, R. / Xu, M. / Skrisovska, L. / Emeson, R.B. / Allain, F.H.-T.
CitationJournal: Structure / Year: 2006
Title: Structure and specific RNA binding of ADAR2 double-stranded RNA binding motifs.
Authors: Stefl, R. / Xu, M. / Skrisovska, L. / Emeson, R.B. / Allain, F.H.-T.
History
DepositionOct 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 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: Double-stranded RNA-specific editase 1


Theoretical massNumber of molelcules
Total (without water)7,9221
Polymers7,9221
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 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Double-stranded RNA-specific editase 1 / dsRNA adenosine deaminase / RNA editing deaminase 1 / RNA editing enzyme 1


Mass: 7922.332 Da / Num. of mol.: 1 / Fragment: double-stranded RNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Adarb1, Red1 / Plasmid: pET16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P51400, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-SEPARATED NOESY
1313D 13C-SEPARATED NOESY
14115N-HSQC
15113C-HSQC
161HNCA
171HNCO
181CBCA(CO)NH
1913D (H)CCH-TOCSY
11012D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N; 200mM NaCl; 50 mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
21mM U-15N,13C; 200mM NaCl; 50 mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
31mM U-15N; 200mM NaCl; 50 mM phosphate buffer, 100% D2O100% D2O
Sample conditionsIonic strength: 250mM total salt / pH: 8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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Processing

NMR softwareName: DYANA, SPARKY, Amber / Version: 7 / Developer: Case, D.A., et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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