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- PDB-2l54: Solution structure of the Zalpha domain mutant of ADAR1 (N43A,Y47A) -

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Basic information

Entry
Database: PDB / ID: 2l54
TitleSolution structure of the Zalpha domain mutant of ADAR1 (N43A,Y47A)
ComponentsDouble-stranded RNA-specific adenosine deaminase
KeywordsHYDROLASE
Function / homology
Function and homology information


somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing ...somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / hematopoietic stem cell homeostasis / response to interferon-alpha / adenosine to inosine editing / RISC complex assembly / negative regulation of hepatocyte apoptotic process / pre-miRNA processing / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / positive regulation of viral genome replication / RNA processing / hematopoietic progenitor cell differentiation / protein export from nucleus / erythrocyte differentiation / response to virus / PKR-mediated signaling / mRNA processing / cellular response to virus / osteoblast differentiation / protein import into nucleus / Interferon alpha/beta signaling / double-stranded RNA binding / defense response to virus / innate immune response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Z-binding domain profile. / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Z-binding domain / Adenosine deaminase z-alpha domain ...ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Z-binding domain profile. / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Z-binding domain / Adenosine deaminase z-alpha domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZhao, J. / Pervushin, K. / Feng, S. / Droge, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Alternate rRNA secondary structures as regulators of translation
Authors: Feng, S. / Li, H. / Zhao, J. / Pervushin, K. / Lowenhaupt, K. / Schwartz, T.U. / Droge, P.
History
DepositionOct 24, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: 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_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_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Double-stranded RNA-specific adenosine deaminase


Theoretical massNumber of molelcules
Total (without water)6,9431
Polymers6,9431
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 / 140target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Double-stranded RNA-specific adenosine deaminase / DRADA / 136 kDa double-stranded RNA-binding protein / p136 / Interferon-inducible protein 4 / IFI-4 / K88DSRBP


Mass: 6943.069 Da / Num. of mol.: 1 / Fragment: DRADA 1 domain, UNP residues 136-198 / Mutation: N43A, Y47A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR, ADAR1, DSRAD, G1P1, IFI4 / Production host: Escherichia coli (E. coli)
References: UniProt: P55265, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D 1H-15N NOESY
1412D 1H-1H TOCSY
1512D 1H-1H NOESY

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Sample preparation

DetailsContents: 50 mM sodium phosphate-1, 50 mM sodium chloride-2, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium phosphate-11
50 mMsodium chloride-21
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 140 / Conformers submitted total number: 20 / Representative conformer: 1

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