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- PDB-7sz3: Mouse PARP13/ZAP ZnF5-WWE1-WWE2 bound to ADPr -

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Basic information

Entry
Database: PDB / ID: 7sz3
TitleMouse PARP13/ZAP ZnF5-WWE1-WWE2 bound to ADPr
ComponentsZinc finger CCCH-type antiviral protein 1
KeywordsANTIVIRAL PROTEIN / PARP13 / ZAP / WWE / ADPr / Poly-ADPribose
Function / homology
Function and homology information


positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / DEAD/H-box RNA helicase binding / regulation of defense response to virus by host / cellular response to exogenous dsRNA / negative regulation of viral genome replication / NAD+-protein ADP-ribosyltransferase activity / positive regulation of type I interferon production / NAD+-protein poly-ADP-ribosyltransferase activity / response to virus ...positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / DEAD/H-box RNA helicase binding / regulation of defense response to virus by host / cellular response to exogenous dsRNA / negative regulation of viral genome replication / NAD+-protein ADP-ribosyltransferase activity / positive regulation of type I interferon production / NAD+-protein poly-ADP-ribosyltransferase activity / response to virus / cellular response to virus / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / innate immune response / RNA binding / identical protein binding / nucleus / metal ion binding / 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 ...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. / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / PHOSPHATE ION / Zinc finger CCCH-type antiviral protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsAyanath Kuttiyatveetil, J.R. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Cell Rep / Year: 2022
Title: Crystal structures and functional analysis of the ZnF5-WWE1-WWE2 region of PARP13/ZAP define a distinctive mode of engaging poly(ADP-ribose).
Authors: Kuttiyatveetil, J.R.A. / Soufari, H. / Dasovich, M. / Uribe, I.R. / Mirhasan, M. / Cheng, S.J. / Leung, A.K.L. / Pascal, J.M.
History
DepositionNov 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,38313
Polymers47,4162
Non-polymers1,96811
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-77 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.415, 87.415, 128.741
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-830-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 485 - 666 / Label seq-ID: 10 - 191

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Zinc finger CCCH-type antiviral protein 1 / ADP-ribosyltransferase diphtheria toxin-like 13 / ARTD13 / Inactive Poly [ADP-ribose] polymerase 13 / PARP13


Mass: 23707.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zc3hav1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UPF5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.4 M Na/K phosphate pH 5.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18057 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18057 Å / Relative weight: 1
ReflectionResolution: 2.2→49.04 Å / Num. obs: 29530 / % possible obs: 100 % / Redundancy: 21.9 % / CC1/2: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.018 / Rrim(I) all: 0.087 / Net I/σ(I): 28.7 / Num. measured all: 648133
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 22.4 % / Rmerge(I) obs: 2.27 / Num. unique obs: 2519 / CC1/2: 0.849 / Rpim(I) all: 0.483 / Rrim(I) all: 2.321 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 11.442 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 2605 8.9 %RANDOM
Rwork0.1926 ---
obs0.1959 26802 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.79 Å2 / Biso mean: 58.912 Å2 / Biso min: 37.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å2-0 Å2
2--1.18 Å20 Å2
3----3.84 Å2
Refinement stepCycle: final / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 119 113 3222
Biso mean--86.42 60.81 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133205
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152825
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.6524356
X-RAY DIFFRACTIONr_angle_other_deg1.2261.5766502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0445352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42721.204191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24115523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5931525
X-RAY DIFFRACTIONr_chiral_restr0.0630.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02820
Refine LS restraints NCS

Ens-ID: 1 / Number: 5562 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 182 -
Rwork0.38 1915 -
all-2097 -
obs--98.31 %
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)
10.17480.17750.7981.87990.00254.843-0.08990.00810.0852-0.150.09610.2845-0.4733-0.008-0.00620.09270.0010.00980.01370.01230.20219.327664.491143.8876
20.5654-0.30120.83471.11470.18134.46330.01390.1221-0.11580.01780.018-0.03010.12380.1729-0.03190.00410.0045-0.00430.0385-0.05210.107516.885547.273752.2587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A485 - 705
2X-RAY DIFFRACTION2B486 - 701

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