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- PDB-2l3j: The solution structure of the ADAR2 dsRBM-RNA complex reveals a s... -

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Basic information

Entry
Database: PDB / ID: 2l3j
TitleThe solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific read out of the minor groove
Components
  • Double-stranded RNA-specific editase 1
  • RNA (71-MER)
KeywordsHydrolase/RNA / editing / dsRNA recognition / dsRBM / Hydrolase-RNA complex
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 / tRNA-specific adenosine deaminase activity / mRNA modification ...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 / tRNA-specific adenosine deaminase activity / mRNA modification / 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 / adenosine to inosine editing / neuromuscular synaptic transmission / innervation / 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
RNA / RNA (> 10) / Double-stranded RNA-specific editase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsStefl, R. / Oberstrass, F.C. / Allain, F.H.-T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove.
Authors: Stefl, R. / Oberstrass, F.C. / Hood, J.L. / Jourdan, M. / Zimmermann, M. / Skrisovska, L. / Maris, C. / Peng, L. / Hofr, C. / Emeson, R.B. / Allain, F.H.
History
DepositionSep 14, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-stranded RNA-specific editase 1
B: RNA (71-MER)


Theoretical massNumber of molelcules
Total (without water)48,2362
Polymers48,2362
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)19 / 40structures with the lowest energy
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: 25447.760 Da / Num. of mol.: 1 / Fragment: UNP residues 74-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Adarb1, Red1 / Production host: Escherichia coli (E. coli)
References: UniProt: P51400, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: RNA chain RNA (71-MER)


Mass: 22788.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: T7 bacteriophage (virus)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N TROSY temp compensated

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Sample preparation

DetailsContents: 1 mM [U-100% 15N] entity_1-1, 1 mM RNA (71-MER)-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 15N]1
1 mMRNA (71-MER)-21
Sample conditionsIonic strength: 0 / pH: 7.6 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 19

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