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- PDB-4ka4: Crystal structure of a proteolytically defined Zbeta domain of hu... -

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Basic information

Entry
Database: PDB / ID: 4ka4
TitleCrystal structure of a proteolytically defined Zbeta domain of human DAI (ZBP1, DLM-1)
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
  • Z-DNA-binding protein 1
KeywordsDNA Binding Protein/DNA / wHTH / DNA sensor / Z-DNA binding / 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 / 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
DNA / Z-DNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAthanasiadis, A. / de Rosa, M. / De Sanctis, D.
CitationJournal: To be Published
Title: Crystal structure of a proteolytically defined Zbeta domain of human DAI (ZBP1, DLM-1)
Authors: Athanasiadis, A. / de Rosa, M. / De Sanctis, D.
History
DepositionApr 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: Z-DNA-binding protein 1
E: Z-DNA-binding protein 1
C: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
G: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
H: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)41,4638
Polymers41,4638
Non-polymers00
Water1086
1
A: Z-DNA-binding protein 1
D: Z-DNA-binding protein 1
C: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
H: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)20,7324
Polymers20,7324
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-21 kcal/mol
Surface area8970 Å2
MethodPISA
2
B: Z-DNA-binding protein 1
E: Z-DNA-binding protein 1
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
G: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)20,7324
Polymers20,7324
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-18 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.647, 63.208, 94.541
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: 8251.354 Da / Num. of mol.: 4 / Fragment: second Zalpha domain Zbeta, UNP RESIDUES 96-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBP1, C20orf183, DLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H171
#2: DNA chain
DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Mass: 2114.398 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 8% PEG 8000, 0.1M sodium acetate, 20% glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2010
RadiationMonochromator: Silicon 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.6→47.27 Å / Num. all: 10325 / Num. obs: 10291 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 65.161 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.6 / % possible all: 96.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYI

3eyi


Resolution: 2.6→47.27 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3017 1024 10 %
Rwork0.2477 --
obs0.2529 10244 98.85 %
Refinement stepCycle: LAST / Resolution: 2.6→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 493 0 6 2359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012434
X-RAY DIFFRACTIONf_angle_d0.553375
X-RAY DIFFRACTIONf_dihedral_angle_d15.664931
X-RAY DIFFRACTIONf_chiral_restr0.036379
X-RAY DIFFRACTIONf_plane_restr0.001350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.73710.3891390.3266124796
2.7371-2.90850.30151430.2931129099
2.9085-3.13310.35051450.2915130399
3.1331-3.44830.32181450.26411311100
3.4483-3.9470.27481470.2309132199
3.947-4.9720.28091490.21311336100
4.972-47.27830.29061560.2388141299

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