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- PDB-2l3c: Solution structure of ADAR2 dsRBM1 bound to LSL RNA -

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Basic information

Entry
Database: PDB / ID: 2l3c
TitleSolution structure of ADAR2 dsRBM1 bound to LSL RNA
Components
  • Double-stranded RNA-specific editase 1
  • RNA (34-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 neuron apoptotic process / motor behavior / 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 / metal ion binding / nucleus / 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
AuthorsAllain, F. / Stefl, R. / Oberstrass, F.
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 12, 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
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

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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 (34-MER)


Theoretical massNumber of molelcules
Total (without water)18,9002
Polymers18,9002
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #18lowest 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: 8036.435 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 74-147
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 (34-MER)


Mass: 10863.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli)

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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
1323D HNCA
1423D HN(CO)CA
1523D HN(CA)CB
1612D 1H-1H TOCSY
1723D (H)CCH-TOCSY
1813D 1H-15N NOESY
1923D 1H-13C NOESY
11052D 1H-13C HSQC
11162D 1H-13C HSQC
11253D 1H-13C NOESY
11363D 1H-13C NOESY
11443D 1H-13C filtered-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] protein-1, 1 mM USL RNA-2, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein-3, 1 mM USL RNA-4, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 15N] protein-5, 1 mM USL RNA-6, 100% D2O100% D2O
41 mM [U-100% 13C; U-100% 15N] protein-7, 1 mM USL RNA-8, 100% D2O100% D2O
51 mM [U-100% 15N] protein-9, 1 mM [U-13C; U-15N]-Gua,Ura USL RNA-10, 100% D2O100% D2O
61 mM [U-100% 15N] protein-11, 1 mM [U-13C; U-15N]-Ade,Cyt USL RNA-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-15N]1
1 mMUSL RNA-21
1 mMprotein-3[U-100% 13C; U-100% 15N]2
1 mMUSL RNA-42
1 mMprotein-5[U-100% 15N]3
1 mMUSL RNA-63
1 mMprotein-7[U-100% 13C; U-100% 15N]4
1 mMUSL RNA-84
1 mMprotein-9[U-100% 15N]5
1 mMUSL RNA-10[U-13C; U-15N]-Gua,Ura5
1 mMprotein-11[U-100% 15N]6
1 mMUSL RNA-12[U-13C; U-15N]-Ade,Cyt6
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 7.6 ambient 310 K
20 7.6 AMBIENT 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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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: 20

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