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- PDB-1oyi: Solution structure of the Z-DNA binding domain of the vaccinia vi... -

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Basic information

Entry
Database: PDB / ID: 1oyi
TitleSolution structure of the Z-DNA binding domain of the vaccinia virus gene E3L
Componentsdouble-stranded RNA-binding protein
KeywordsVIRAL PROTEIN / (alpha+beta) helix-turn-helix
Function / homology
Function and homology information


double-stranded RNA adenosine deaminase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host PKR/eIFalpha signaling / symbiont-mediated perturbation of host apoptosis / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / RNA binding
Similarity search - Function
Protein E3 / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / 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 ...Protein E3 / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / 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-binding protein
Similarity search - Component
Biological speciesVaccinia virus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKahmann, J.D. / Wecking, D.A. / Putter, V. / Lowenhaupt, K. / Kim, Y.-G. / Schmieder, P. / Oschkinat, H. / Rich, A. / Schade, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The solution structure of the N-terminal domain of E3L shows a tyrosine conformation that may explain its reduced affinity to Z-DNA in vitro.
Authors: Kahmann, J.D. / Wecking, D.A. / Putter, V. / Lowenhaupt, K. / Kim, Y.-G. / Schmieder, P. / Oschkinat, H. / Rich, A. / Schade, M.
History
DepositionApr 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE THESE RESIDUES ARE VECTOR-ENCODED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: double-stranded RNA-binding protein


Theoretical massNumber of molelcules
Total (without water)9,1921
Polymers9,1921
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 / 45020 structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein double-stranded RNA-binding protein


Mass: 9192.250 Da / Num. of mol.: 1 / Fragment: Z-DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Gene: E3L / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q86638

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
NMR detailsText: resonance assignments were obtained from triple-resonance NMR spectra and 3D 15N-separated NOESY spectra

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Sample preparation

Details
Solution-IDContentsSolvent system
12.2 mM U-15N E3L20 mM Na-phosphate pH=6.5; 20 mM NaCl; 5% D2O
22 mM U-13C,15N E3L20 mM Na-phosphate pH=6.5; 20 mM NaCl; 100 % D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Neidig, R.collection
Sparky3.1Goddard, T.D. and Kneller, D.G.data analysis
DYANA1.5Guntert, P.structure solution
DYANA1.5Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures with the lowest energy
Conformers calculated total number: 450 / Conformers submitted total number: 20

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