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- PDB-2mdr: Solution structure of the third double-stranded RNA-binding domai... -

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Basic information

Entry
Database: PDB / ID: 2mdr
TitleSolution structure of the third double-stranded RNA-binding domain (dsRBD3) of human adenosine-deaminase ADAR1
ComponentsDouble-stranded RNA-specific adenosine deaminase
KeywordsHYDROLASE / deaminase
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 / pre-miRNA processing / negative regulation of hepatocyte apoptotic process / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / positive regulation of viral genome replication / hematopoietic progenitor cell differentiation / RNA processing / protein export from nucleus / erythrocyte differentiation / response to virus / PKR-mediated signaling / cellular response to virus / mRNA processing / osteoblast differentiation / protein import into nucleus / double-stranded RNA binding / Interferon alpha/beta signaling / defense response to virus / innate immune response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
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 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBarraud, P. / Banerjee, S. / Mohamed, W.I. / Jantsch, M.F. / Allain, F.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1.
Authors: Barraud, P. / Banerjee, S. / Mohamed, W.I. / Jantsch, M.F. / Allain, F.H.
History
DepositionSep 17, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: 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 adenosine deaminase


Theoretical massNumber of molelcules
Total (without water)12,4921
Polymers12,4921
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 / 100structures with the lowest energy
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: 12492.193 Da / Num. of mol.: 1 / Fragment: UNP residues 708-801
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) / Strain (production host): BL21(DE3)codon+RIL
References: UniProt: P55265, double-stranded RNA adenine deaminase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aliphatic
1413D HNCA
1513D CBCA(CO)NH
1613D HN(CA)CB
1723D (H)CCH-TOCSY
1842D 1H-1H NOESY
1942D 1H-1H TOCSY
11033D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
113315N{1H}-HeteroNOE
1143long-range 2D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-0.9 mM [U-99% 13C; U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.7-0.9 mM [U-99% 13C; U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 100% D2O100% D2O
30.7-0.9 mM [U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
40.7-0.9 mM dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMdsRBD3-1[U-99% 13C; U-99% 15N]0.7-0.91
20 mMsodium phosphate-21
100 mMpotassium chloride-31
1 mMDTT-41
mMdsRBD3-5[U-99% 13C; U-99% 15N]0.7-0.92
20 mMsodium phosphate-62
100 mMpotassium chloride-72
1 mMDTT-82
mMdsRBD3-9[U-99% 15N]0.7-0.93
20 mMsodium phosphate-103
100 mMpotassium chloride-113
1 mMDTT-123
mMdsRBD3-130.7-0.94
20 mMsodium phosphate-144
100 mMpotassium chloride-154
1 mMDTT-164
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 313.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE7504
Bruker AvanceBrukerAVANCE9005

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckNMRLaskowski and MacArthurstructure validation
CINGNabuurs, Spronk, Krieger, Maassen, Vriend and Vuisterstructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2165 / NOE intraresidue total count: 430 / NOE long range total count: 704 / NOE medium range total count: 507 / NOE sequential total count: 524 / Hydrogen bond constraints total count: 98
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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