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- PDB-2ljh: NMR structure of Double-stranded RNA-specific editase Adar -

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Basic information

Entry
Database: PDB / ID: 2ljh
TitleNMR structure of Double-stranded RNA-specific editase Adar
ComponentsDouble-stranded RNA-specific editase Adar
KeywordsHYDROLASE / dsRBD / dsRBM / editing
Function / homology
Function and homology information


C6 deamination of adenosine / Formation of editosomes by ADAR proteins / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / regulation of miRNA-mediated gene silencing / RNA modification / tRNA-specific adenosine deaminase activity / mRNA modification / double-stranded RNA adenosine deaminase activity / male courtship behavior / adenosine to inosine editing ...C6 deamination of adenosine / Formation of editosomes by ADAR proteins / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / regulation of miRNA-mediated gene silencing / RNA modification / tRNA-specific adenosine deaminase activity / mRNA modification / double-stranded RNA adenosine deaminase activity / male courtship behavior / adenosine to inosine editing / adult behavior / locomotor rhythm / RNA processing / adult locomotory behavior / locomotory behavior / regulation of membrane potential / regulation of circadian rhythm / mRNA processing / double-stranded RNA binding / response to heat / response to oxidative stress / response to hypoxia / nucleolus / nucleus / metal ion binding / cytoplasm
Similarity search - Function
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 ...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 Adar
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsBarraud, P. / Allain, F.H.-T.
CitationJournal: Biochimie / Year: 2012
Title: Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA.
Authors: Barraud, P. / Heale, B.S. / O'Connell, M.A. / Allain, F.H.
History
DepositionSep 13, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: 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: Double-stranded RNA-specific editase Adar


Theoretical massNumber of molelcules
Total (without water)12,5651
Polymers12,5651
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Double-stranded RNA-specific editase Adar / Adenosine deaminase that act on RNA / Pre-mRNA adenosine deaminase / RNA-editing deaminase 1 / RNA- ...Adenosine deaminase that act on RNA / Pre-mRNA adenosine deaminase / RNA-editing deaminase 1 / RNA-editing enzyme 1 / dADAR / dsRNA adenosine deaminase


Mass: 12564.591 Da / Num. of mol.: 1 / Fragment: DRBM 1 domain residues 48-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Adar, hypnos-2, CG12598 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL
References: UniProt: Q9NII1, 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 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1423D HNCA
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D (H)CCH-TOCSY
1823D H(CCO)NH
1913D 1H-15N NOESY
11023D 1H-13C NOESY aliphatic
11123D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.2 mM [U-15N] dADAR-dsRBD1, 90% H2O/10% D2O90% H2O/10% D2O
20.8-1.2 mM [U-13C; U-15N] dADAR-dsRBD1, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMdADAR-dsRBD1-1[U-15N]0.8-1.21
mMdADAR-dsRBD1-2[U-13C; U-15N]0.8-1.22
Sample conditionsIonic strength: 25 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2208 / NOE intraresidue total count: 435 / NOE long range total count: 726 / NOE medium range total count: 484 / NOE sequential total count: 563 / Hydrogen bond constraints total count: 64
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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