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- PDB-7v2z: ZIKV NS3helicase in complex with ssRNA and ATP-Mn2+ -

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Basic information

Entry
Database: PDB / ID: 7v2z
TitleZIKV NS3helicase in complex with ssRNA and ATP-Mn2+
Components
  • Core protein
  • RNA (5'-R(*AP*GP*AP*UP*C)-3')
KeywordsVIRAL PROTEIN / ZIKV NS3helicase
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / serine-type endopeptidase activity ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / RNA / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10101667251 Å
AuthorsLin, M.M. / Yang, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81772204 China
Citation
Journal: Acs Infect Dis. / Year: 2022
Title: Structural Basis of Zika Virus Helicase in RNA Unwinding and ATP Hydrolysis.
Authors: Lin, M. / Cui, W. / Tian, H. / Zhang, Y. / Chen, C. / Yang, X. / Chi, H. / Mu, Z. / Chen, C. / Wang, Z. / Ji, X. / Yang, H. / Lin, Z.
#1: Journal: To Be Published
Title: Structure of ZIKV NS3helicase in complex of ssRNA and ATP-Mn2+ at 2.1 Angstroms resolution
Authors: Lin, M.M. / Yang, H.T.
History
DepositionAug 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Mar 1, 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 1.3Nov 29, 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: Core protein
B: RNA (5'-R(*AP*GP*AP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7204
Polymers51,1582
Non-polymers5622
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-14 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.620, 72.356, 59.507
Angle α, β, γ (deg.)90.000, 94.154, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 49587.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1B0YUR2, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: RNA chain RNA (5'-R(*AP*GP*AP*UP*C)-3')


Mass: 1570.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sodium tartrate tetrahydrate pH 7.4 and 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→45.89 Å / Num. obs: 25785 / % possible obs: 97.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 2.72
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.443 / Num. unique obs: 1307

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMT

5jmt


Resolution: 2.10101667251→40.809811361 Å / SU ML: 0.248772722078 / Cross valid method: FREE R-VALUE / σ(F): 1.34895096599 / Phase error: 27.3925161256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239342529292 1156 4.56520022115 %
Rwork0.188683533629 24166 -
obs0.191042529433 25322 97.0749472877 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.0964759979 Å2
Refinement stepCycle: LAST / Resolution: 2.10101667251→40.809811361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 104 15 348 3946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006891888048033685
X-RAY DIFFRACTIONf_angle_d0.8769593831555020
X-RAY DIFFRACTIONf_chiral_restr0.0520946964165558
X-RAY DIFFRACTIONf_plane_restr0.00606916087795630
X-RAY DIFFRACTIONf_dihedral_angle_d9.392898218992218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.19660.4186217579291410.3986564308522916X-RAY DIFFRACTION93.6007348438
2.1966-2.31240.3233092373451230.2719343641732667X-RAY DIFFRACTION86.8347338936
2.3124-2.45730.2878288008751360.2045721996023122X-RAY DIFFRACTION100
2.4573-2.6470.2863096860631640.2000747943993093X-RAY DIFFRACTION100
2.647-2.91330.2702283673041430.1998412689473087X-RAY DIFFRACTION100
2.9133-3.33470.2606581027761660.1871389841033111X-RAY DIFFRACTION100
3.3347-4.20070.2019668259881340.1562141232442994X-RAY DIFFRACTION96.2757771622
4.2007-40.8080.1617187590151490.1507277419863176X-RAY DIFFRACTION99.700149925

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