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- PDB-2l4m: Solution structure of the Zbeta domain of human DAI and its bindi... -

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Basic information

Entry
Database: PDB / ID: 2l4m
TitleSolution structure of the Zbeta domain of human DAI and its binding modes to B- and Z-DNA
ComponentsUncharacterized protein
KeywordsDNA BINDING PROTEIN / Zbeta / Z-DNA binding protein / bent alpha helix / alpha+beta helix-turn-helix / B-Z transition
Function / homology
Function and homology information


ZBP1(DAI) mediated induction of type I IFNs / left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / IRF3 mediated activation of type 1 IFN / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / antiviral innate immune response ...ZBP1(DAI) mediated induction of type I IFNs / left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / IRF3 mediated activation of type 1 IFN / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / antiviral innate immune response / defense response to fungus / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / positive regulation of inflammatory response / double-stranded RNA binding / regulation of inflammatory response / defense response to virus / Potential therapeutics for SARS / positive regulation of apoptotic process / apoptotic process / DNA binding / RNA binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Z-DNA-binding protein 1 / RHIM domain / RIP homotypic interaction motif / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Z-DNA-binding protein 1 / RHIM domain / RIP homotypic interaction motif / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha 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
: / Z-DNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 5
AuthorsKim, K. / Khayrutdinov, B.I. / Jeon, Y.H. / Kim, K.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Solution structure of the Zbeta domain of human DNA-dependent activator of IFN-regulatory factors and its binding modes to B- and Z-DNA
Authors: Kim, K. / Khayrutdinov, B. / Lee, C.-K. / Cheong, H.-K. / Kang, S. / Park, H. / Lee, S. / Kim, Y.-G. / Jee, J.-G. / Rich, A. / Kim, K.K. / Jeon, Y.H.
History
DepositionOct 8, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 13, 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)8,2271
Polymers8,2271
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein / DAI / DNA-dependent activator of IFN-regulatory factors


Mass: 8227.364 Da / Num. of mol.: 1 / Fragment: UNP residues 103-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBP1 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9J523, UniProt: Q9H171*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HN(CO)CA
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY
11313D 1H-15N NOESY
11413D 1H-15N TOCSY
11513D 1H-13C NOESY

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Sample preparation

DetailsContents: 2 mM [U-99% 13C; U-99% 15N] ZbetaDAI-1, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: ZbetaDAI-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 10 / pH: 5.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 5

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