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- PDB-4x52: Human PARP13 (ZC3HAV1), C-Terminal PARP Domain (H810N; N830Y variant) -

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Basic information

Entry
Database: PDB / ID: 4x52
TitleHuman PARP13 (ZC3HAV1), C-Terminal PARP Domain (H810N; N830Y variant)
ComponentsZinc finger CCCH-type antiviral protein 1
KeywordsIMMUNE SYSTEM / ANTIVIRAL DEFENSE / PARP / ZAP / MUTANT
Function / homology
Function and homology information


positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / negative regulation of viral genome replication / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of interferon-beta production / response to virus / Signaling by BRAF and RAF1 fusions / defense response to virus / positive regulation of canonical NF-kappaB signal transduction ...positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / negative regulation of viral genome replication / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of interferon-beta production / response to virus / Signaling by BRAF and RAF1 fusions / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / cadherin binding / innate immune response / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ZAP, zinc finger / ZAP, helix turn helix N-terminal domain / Zap helix turn helix N-terminal domain / Zinc-finger antiviral protein (ZAP) zinc finger domain 3 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...ZAP, zinc finger / ZAP, helix turn helix N-terminal domain / Zap helix turn helix N-terminal domain / Zinc-finger antiviral protein (ZAP) zinc finger domain 3 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Zinc finger CCCH-type antiviral protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Klepsch, M. / Schuler, H.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Foundation for Strategic Research Sweden
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Lack of ADP-ribosyltransferase Activity in Poly(ADP-ribose) Polymerase-13/Zinc Finger Antiviral Protein.
Authors: Karlberg, T. / Klepsch, M. / Thorsell, A.G. / Andersson, C.D. / Linusson, A. / Schuler, H.
History
DepositionDec 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: 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: Zinc finger CCCH-type antiviral protein 1
B: Zinc finger CCCH-type antiviral protein 1
C: Zinc finger CCCH-type antiviral protein 1
D: Zinc finger CCCH-type antiviral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9859
Polymers81,5134
Non-polymers4725
Water2,468137
1
A: Zinc finger CCCH-type antiviral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5663
Polymers20,3781
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zinc finger CCCH-type antiviral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4742
Polymers20,3781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Zinc finger CCCH-type antiviral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4742
Polymers20,3781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Zinc finger CCCH-type antiviral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4702
Polymers20,3781
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.930, 50.000, 153.630
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Zinc finger CCCH-type antiviral protein 1 / ADP-ribosyltransferase diphtheria toxin-like 13 / ARTD13 / Zinc finger CCCH domain-containing ...ADP-ribosyltransferase diphtheria toxin-like 13 / ARTD13 / Zinc finger CCCH domain-containing protein 2 / Zinc finger antiviral protein / ZAP


Mass: 20378.238 Da / Num. of mol.: 4 / Mutation: H810N, N830Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZC3HAV1, ZC3HDC2, PRO1677 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 pRARE / References: UniProt: Q7Z2W4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 25% PEG3350, 0.4M Ammonium sulfate, 0.1M Bis-Tris, 10mM 3-Aminobenzamide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.9077 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9077 Å / Relative weight: 1
ReflectionResolution: 2.08→30 Å / Num. all: 50705 / Num. obs: 50705 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 41.94 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.5
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.5 / % possible all: 95.4

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2x5y

2x5y


Resolution: 2.08→29.7 Å / Cor.coef. Fo:Fc: 0.9401 / Cor.coef. Fo:Fc free: 0.9304 / SU R Cruickshank DPI: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2536 5 %RANDOM
Rwork0.2132 ---
obs0.2142 50704 99.43 %-
Displacement parametersBiso mean: 56.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.8233 Å20 Å2-3.5203 Å2
2---8.6522 Å20 Å2
3---6.8288 Å2
Refine analyzeLuzzati coordinate error obs: 0.418 Å
Refinement stepCycle: 1 / Resolution: 2.08→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5718 0 27 137 5882
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125906HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077975HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2729SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes834HARMONIC5
X-RAY DIFFRACTIONt_it5906HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion3.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion740SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6621SEMIHARMONIC4
LS refinement shellResolution: 2.08→2.13 Å
RfactorNum. reflection% reflection
Rfree0.2709 178 5.02 %
Rwork0.2637 3370 -
obs--99.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.00140.8468-0.43522.17340.53074.29450.1288-0.16570.08660.0175-0.00620.01380.2719-0.1302-0.1226-0.08650.0021-0.029-0.1165-0.0431-0.0718-31.26564.017113.6056
24.65330.3141-1.09131.531-0.08854.9009-0.1669-0.6870.22030.07470.1966-0.1638-0.2430.3913-0.0297-0.1767-0.1746-0.00360.0949-0.1364-0.2996-13.137222.9958.7203
37.4890.9241.48351.96970.67053.71130.44560.5487-0.1904-0.0113-0.1832-0.07250.16860.7146-0.2624-0.25630.018-0.0352-0.0182-0.0634-0.2314-4.356113.208921.2121
42.21530.63910.9182.19411.16215.58750.05-0.2630.01750.4591-0.2280.27820.728-0.52850.178-0.0756-0.29060.13290.0343-0.0959-0.2792-36.31556.216352.9753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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