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- PDB-2l2k: Solution NMR structure of the R/G STEM LOOP RNA-ADAR2 DSRBM2 Complex -

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Basic information

Entry
Database: PDB / ID: 2l2k
TitleSolution NMR structure of the R/G STEM LOOP RNA-ADAR2 DSRBM2 Complex
Components
  • Adenosine deaminase
  • RNA (42-MER)
KeywordsHydrolase/rna / AC MISMATCH / RNA EDITING / DSRBM / STEMLOOP / 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 / cytosol
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
RNA / RNA (> 10) / Double-stranded RNA-specific editase 1 / Double-stranded RNA-specific editase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAllain, F.H.-T. / Oberstrass, F.C. / Stefl, R.
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
DepositionAug 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Adenosine deaminase
A: RNA (42-MER)


Theoretical massNumber of molelcules
Total (without water)21,1742
Polymers21,1742
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Adenosine deaminase / RNA-specific / B1 / isoform CRA_d


Mass: 7703.832 Da / Num. of mol.: 1 / Fragment: unp residues 231-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ADAR2, Adarb1, mCG_3378, RED1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+RIL
References: UniProt: Q3UHM7, UniProt: Q91ZS8*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: RNA chain RNA (42-MER)


Mass: 13470.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY-WATER
1222D-NOESY-D2O
1333D 13C-SEPARATED NOESY
1433D 15N -SEPARATED NOESY
1512D 1H-1H TOCSY
1633D 1H-13C NOESY
1732D 1H-13C HSQC
1832D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] complex-1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] complex-2, 100% D2O100% D2O
31 mM [U-100% 15N] complex-3, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] complex-4, 100% D2O100% D2O
51 mM [U-100% 13C; U-100% 15N] complex-5, 100% D2O100% D2O
61 mM [U-100% 13C; U-100% 15N] complex-6, 100% D2O100% D2O
71 mM [U-100% 13C; U-100% 15N] complex-7, 100% D2O100% D2O
81 mM [U-100% 13C; U-100% 15N] complex-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMcomplex-1[U-100% 15N]1
1 mMcomplex-2[U-100% 15N]2
1 mMcomplex-3[U-100% 15N]3
1 mMcomplex-4[U-100% 13C; U-100% 15N]4
1 mMcomplex-5[U-100% 13C; U-100% 15N]5
1 mMcomplex-6[U-100% 13C; U-100% 15N]6
1 mMcomplex-7[U-100% 13C; U-100% 15N]7
1 mMcomplex-8[U-100% 13C; U-100% 15N]8
Sample conditionsIonic strength: 20 / pH: 7.6 / Pressure: AMBIENT / Temperature: 278 K

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NMR measurement

NMR spectrometerType: BRUKER DRX, AVNACE / Manufacturer: Bruker / Model: DRX, AVNACE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AmberCASE, D.A. ET AL.refinement
TopSpin2Bruker Biospinstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
PROCHECKNMRLaskowski and MacArthurstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CYANA-AMBER REFINEMENT
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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