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- PDB-3eyi: The crystal structure of the second Z-DNA binding domain of human... -

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Basic information

Entry
Database: PDB / ID: 3eyi
TitleThe crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA
Components
  • 5'-TCGCGCG-3'
  • Z-DNA-binding protein 1
KeywordsDNA Binding Protein/DNA / Alternative splicing / DNA-binding / Polymorphism / DNA Binding Protein-Z-DNA COMPLEX / DNA Binding Protein-DNA COMPLEX
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 / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / 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
DNA / Z-DNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsHa, S.C. / Kim, K.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA.
Authors: Ha, S.C. / Kim, D. / Hwang, H.Y. / Rich, A. / Kim, Y.G. / Kim, K.K.
History
DepositionOct 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Z-DNA-binding protein 1
B: Z-DNA-binding protein 1
C: 5'-TCGCGCG-3'
D: 5'-TCGCGCG-3'


Theoretical massNumber of molelcules
Total (without water)21,6374
Polymers21,6374
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-20 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.530, 58.249, 88.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Z-DNA-binding protein 1 / Tumor stroma and activated macrophage protein DLM-1


Mass: 8703.931 Da / Num. of mol.: 2 / Fragment: The second Z-DNA binding domain (Zbeta)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf183, DLM1, ZBP1, ZBP1/DLM1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H171
#2: DNA chain 5'-TCGCGCG-3'


Mass: 2114.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The Z-DNA is chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 31-33% PEG 4000, 200-260 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCl11
2PEG 400011
3sodium acetate11
4Tris-HCl12
5PEG 400012
6sodium acetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9795, 0.9798, 0.9721
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.97211
ReflectionResolution: 1.45→50 Å / Num. all: 27940 / Num. obs: 26766 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.075
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 8.9 / Num. unique all: 2301 / % possible all: 84.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
autoSHARPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.349 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 2617 9.9 %RANDOM
Rwork0.15322 ---
all0.15719 26420 --
obs0.15719 23803 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.757 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 263 0 351 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211405
X-RAY DIFFRACTIONr_angle_refined_deg1.6492.1891932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575127
X-RAY DIFFRACTIONr_chiral_restr0.0910.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02980
X-RAY DIFFRACTIONr_nbd_refined0.2750.2624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.267
X-RAY DIFFRACTIONr_mcbond_it0.971.5653
X-RAY DIFFRACTIONr_mcangle_it1.75521039
X-RAY DIFFRACTIONr_scbond_it2.4133752
X-RAY DIFFRACTIONr_scangle_it3.444.5893
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 182
Rwork0.198 1678

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