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- PDB-6uej: Crystal structure of human zinc finger antiviral protein bound to RNA -

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Basic information

Entry
Database: PDB / ID: 6uej
TitleCrystal structure of human zinc finger antiviral protein bound to RNA
Components
  • RNA (5'-R(P*UP*CP*G)-3')
  • Zinc finger CCCH-type antiviral protein 1
KeywordsANTIVIRAL PROTEIN / Zinc Finger Antiviral protein / ZAP / RNA binding domain
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 / positive regulation of canonical NF-kappaB signal transduction / 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 / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / 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. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SPERMINE / RNA / Zinc finger CCCH-type antiviral protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsMeagher, J.L. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI50470 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences.
Authors: Meagher, J.L. / Takata, M. / Goncalves-Carneiro, D. / Keane, S.C. / Rebendenne, A. / Ong, H. / Orr, V.K. / MacDonald, M.R. / Stuckey, J.A. / Bieniasz, P.D. / Smith, J.L.
History
DepositionSep 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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

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Assembly

Deposited unit
A: Zinc finger CCCH-type antiviral protein 1
B: RNA (5'-R(P*UP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3677
Polymers26,9032
Non-polymers4645
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-15 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.090, 123.090, 40.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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: 25991.076 Da / Num. of mol.: 1
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: RNA chain RNA (5'-R(P*UP*CP*G)-3')


Mass: 911.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7% Peg 8000, 30mM magnesium chloride, 10mM spermine, 50mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→40.668 Å / Num. obs: 18081 / % possible obs: 99.8 % / Redundancy: 20.564 % / Biso Wilson estimate: 64.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.081 / Χ2: 1.087 / Net I/σ(I): 20.69 / Num. measured all: 371826
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.3420.8031.3752.0859456289828580.8861.40998.6
2.34-2.521.4640.8463.6958295271627160.9560.867100
2.5-2.721.080.4247.353817255325530.9870.434100
2.7-2.9520.4630.22612.7747780233523350.9960.231100
2.95-3.319.6450.11922.5841373210621060.9980.122100
3.3-3.8121.4930.07638.6140729189518950.9990.078100
3.81-4.6520.6980.05849.4433323161016100.9990.059100
4.65-6.5318.1680.05652.3122946126312630.9990.057100
6.53-40.66818.960.05258.11141067497440.9990.05499.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U9G

3u9g


Resolution: 2.21→38 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.255 957 5.29 %RANDOM
Rwork0.211 ---
obs0.213 18076 99.9 %-
Displacement parametersBiso max: 167.22 Å2 / Biso mean: 75.67 Å2 / Biso min: 43.74 Å2
Baniso -1Baniso -2Baniso -3
1-13.2494 Å20 Å20 Å2
2--13.2494 Å20 Å2
3----26.4987 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.21→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 63 14 93 1816
Biso mean--87.67 73.92 -
Num. residues----215
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d619SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes288HARMONIC5
X-RAY DIFFRACTIONt_it1748HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion227SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance16HARMONIC1
X-RAY DIFFRACTIONt_utility_angle24HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1972SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1748HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2361HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion18.5
LS refinement shellResolution: 2.21→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 47
RfactorNum. reflection% reflection
Rfree0.4125 19 4.94 %
Rwork0.2354 366 -
all0.2448 385 -
obs--96.3 %

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