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- PDB-1qgp: NMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1, 15 STRUCTURES -

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Entry
Database: PDB / ID: 1qgp
TitleNMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1, 15 STRUCTURES
ComponentsPROTEIN (DOUBLE STRANDED RNA ADENOSINE DEAMINASE)
KeywordsHYDROLASE / Z-ALPHA-Z-DNA BINDING DOMAIN / RNA-EDITING / Z-DNA RECOGNITION / ADAR1 / HELIX- TURN-HELIX
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 / molecular dynamics
AuthorsSchade, M. / Turner, C.J. / Kuehne, R. / Schmieder, P. / Lowenhaupt, K. / Herbert, A. / Rich, A. / Oschkinat, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA.
Authors: Schade, M. / Turner, C.J. / Kuhne, R. / Schmieder, P. / Lowenhaupt, K. / Herbert, A. / Rich, A. / Oschkinat, H.
History
DepositionMay 3, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Oct 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (DOUBLE STRANDED RNA ADENOSINE DEAMINASE)


Theoretical massNumber of molelcules
Total (without water)8,6101
Polymers8,6101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein PROTEIN (DOUBLE STRANDED RNA ADENOSINE DEAMINASE)


Mass: 8609.835 Da / Num. of mol.: 1 / Fragment: Z-ALPHA DOMAIN / Mutation: C125S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: HHHHHH HISTIDINE TAG WAS ADDED AT THE N- TERMINUS FOR EASE OF PURIFICATION
Production host: Escherichia coli (E. coli) / References: UniProt: P55265

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY (1H
12113C
13115N)
14115N TOCSY-HSQC
1512D TOCSY
161HCCHTOCSY
171HNCA
181HN(CO)CA
191HN(CA)CB
1101HN(CO)CACB
1111HNCO
1121HN(CA)CO

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Sample preparation

DetailsContents: NA-PHOSPHATE
Sample conditionsIonic strength: 0.137 M NACL / pH: 5.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX750BrukerDMX7507501
Bruker DRX600BrukerDRX6006002
Bruker SELF BUILBrukerSELF BUIL5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
Conformers calculated total number: 200 / Conformers submitted total number: 15

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