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- PDB-7tgq: Zinc finger antiviral protein (ZAP) central domain bound to ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 7tgq
TitleZinc finger antiviral protein (ZAP) central domain bound to ADP-ribose
ComponentsZinc finger CCCH-type antiviral protein 1
KeywordsANTIVIRAL PROTEIN / restriction factor
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 / late endosome / defense response to virus ...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 / late endosome / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / lysosome / cadherin binding / innate immune response / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #50 / 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 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / WWE domain superfamily ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #50 / 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 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / WWE domain superfamily / WWE domain / WWE domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5-DIPHOSPHORIBOSE / Zinc finger CCCH-type antiviral protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPornillos, O.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI150479 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54-AI150470 United States
CitationJournal: Plos Pathog. / Year: 2022
Title: Poly(ADP-ribose) potentiates ZAP antiviral activity.
Authors: Xue, G. / Braczyk, K. / Goncalves-Carneiro, D. / Dawidziak, D.M. / Sanchez, K. / Ong, H. / Wan, Y. / Zadrozny, K.K. / Ganser-Pornillos, B.K. / Bieniasz, P.D. / Pornillos, O.
History
DepositionJan 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: 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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger CCCH-type antiviral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1295
Polymers23,3861
Non-polymers7434
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.958, 89.958, 52.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-857-

HOH

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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 ...ADP-ribosyltransferase diphtheria toxin-like 13 / ARTD13 / Inactive Poly [ADP-ribose] polymerase 13 / PARP13 / Zinc finger CCCH domain-containing protein 2 / Zinc finger antiviral protein / ZAP


Mass: 23386.410 Da / Num. of mol.: 1 / Fragment: central domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZC3HAV1, ZC3HDC2, PRO1677 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z2W4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8-1.1 M sodium nitrate, 0.1 M sodium acetate / PH range: 4.8-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 17745 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 24.12 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.025 / Rrim(I) all: 0.114 / Net I/σ(I): 25.2
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 875 / CC1/2: 0.458 / Rpim(I) all: 0.592 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KZH

7kzh


Resolution: 2→43.71 Å / SU ML: 0.2644 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.6226
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2728 843 5.27 %
Rwork0.2381 15156 -
obs0.2399 15999 90.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.42 Å2
Refinement stepCycle: LAST / Resolution: 2→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 45 75 1566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411534
X-RAY DIFFRACTIONf_angle_d1.03912091
X-RAY DIFFRACTIONf_chiral_restr0.0626223
X-RAY DIFFRACTIONf_plane_restr0.0078258
X-RAY DIFFRACTIONf_dihedral_angle_d6.024197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10.3214820.29371218X-RAY DIFFRACTION44.84
2.1-2.260.28951320.26122746X-RAY DIFFRACTION99.93
2.26-2.490.34791450.29772774X-RAY DIFFRACTION100
2.49-2.850.32811650.27722738X-RAY DIFFRACTION100
2.85-3.590.29691680.23532780X-RAY DIFFRACTION100
3.59-43.710.20081510.19662900X-RAY DIFFRACTION99.87

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