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- PDB-7oj4: Crystal structure of apo NS3 helicase from tick-borne encephaliti... -

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Basic information

Entry
Database: PDB / ID: 7oj4
TitleCrystal structure of apo NS3 helicase from tick-borne encephalitis virus
ComponentsNS3 helicase domain
KeywordsVIRAL PROTEIN / RNA helicase / hydrolase / non-structural protein
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
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. ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.828 Å
AuthorsAnindita, P.D. / Havlickova, P. / Kascakova, B. / Grinkevich, P. / Brynda, J. / Franta, Z.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0./15_003/0000441 Czech Republic
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Mechanistic insight into the RNA-stimulated ATPase activity of tick-borne encephalitis virus helicase.
Authors: Anindita, P.D. / Halbeisen, M. / Reha, D. / Tuma, R. / Franta, Z.
#1: Journal: Biorxiv / Year: 2022
Title: Mechanistic insight into the ATP hydrolysis cycle of tick-borne encephalitis virus helicase
Authors: Anindita, P.D. / Halbeisen, M. / Reha, D. / Tuma, R. / Franta, Z.
History
DepositionMay 13, 2021Deposition site: PDBE / Processing site: PDBE
SupersessionMar 23, 2022ID: 7AY4
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Structure summary / Category: pdbx_contact_author / pdbx_database_related
Revision 1.2Sep 7, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Sep 14, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.5Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS3 helicase domain


Theoretical massNumber of molelcules
Total (without water)53,4891
Polymers53,4891
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.298, 73.298, 196.048
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NS3 helicase domain / Serine protease NS3


Mass: 53489.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: A0A2S1PWV0, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis Tris Propane pH 6.5, 0.2 M Sodium acetate trihydrate, 20% w/v PEG 3350, 10% v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.828→49.06 Å / Num. obs: 48205 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 2.22
Reflection shellResolution: 1.83→1.94 Å / Num. unique obs: 7581 / CC1/2: 0.865 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ADW

6adw


Resolution: 1.828→49.06 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.594 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2291 2366 4.908 %
Rwork0.1808 45839 -
all0.183 --
obs-48205 99.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.029 Å20 Å20 Å2
2---0.029 Å20 Å2
3---0.058 Å2
Refinement stepCycle: LAST / Resolution: 1.828→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 206 3572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133449
X-RAY DIFFRACTIONr_bond_other_d0.0180.0173227
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.6514673
X-RAY DIFFRACTIONr_angle_other_deg1.8021.5867412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6785425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29120.539204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90215581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.651537
X-RAY DIFFRACTIONr_chiral_restr0.1080.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023916
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02834
X-RAY DIFFRACTIONr_nbd_refined0.220.2652
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.22965
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21691
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2143
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0650.23
X-RAY DIFFRACTIONr_nbd_other0.1280.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.26
X-RAY DIFFRACTIONr_mcbond_it8.0034.3061706
X-RAY DIFFRACTIONr_mcbond_other7.9974.3051705
X-RAY DIFFRACTIONr_mcangle_it8.6636.4372129
X-RAY DIFFRACTIONr_mcangle_other8.6626.4382130
X-RAY DIFFRACTIONr_scbond_it9.8554.8261743
X-RAY DIFFRACTIONr_scbond_other9.8534.8271744
X-RAY DIFFRACTIONr_scangle_it10.9126.9652544
X-RAY DIFFRACTIONr_scangle_other10.916.9662545
X-RAY DIFFRACTIONr_lrange_it10.04549.0813817
X-RAY DIFFRACTIONr_lrange_other10.05848.9243789
X-RAY DIFFRACTIONr_rigid_bond_restr9.35836676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.828-1.8760.3591530.2863272X-RAY DIFFRACTION97.9691
1.876-1.9270.3471610.2463282X-RAY DIFFRACTION100
1.927-1.9830.2781630.223146X-RAY DIFFRACTION100
1.983-2.0440.2871560.2063071X-RAY DIFFRACTION100
2.044-2.1110.2641860.2032955X-RAY DIFFRACTION100
2.111-2.1850.231540.1872870X-RAY DIFFRACTION100
2.185-2.2670.2381290.1842805X-RAY DIFFRACTION100
2.267-2.360.221260.1682735X-RAY DIFFRACTION99.9651
2.36-2.4650.2671390.1682573X-RAY DIFFRACTION100
2.465-2.5850.2181100.1672487X-RAY DIFFRACTION100
2.585-2.7250.2581380.1682385X-RAY DIFFRACTION100
2.725-2.890.2621180.1652221X-RAY DIFFRACTION100
2.89-3.090.2341160.1822111X-RAY DIFFRACTION100
3.09-3.3370.2531060.2031995X-RAY DIFFRACTION100
3.337-3.6560.221890.1991838X-RAY DIFFRACTION100
3.656-4.0870.2930.1641671X-RAY DIFFRACTION99.9433
4.087-4.7190.173790.1321491X-RAY DIFFRACTION100
4.719-5.7790.2660.1671285X-RAY DIFFRACTION100
5.779-8.1690.21580.1871027X-RAY DIFFRACTION100
8.169-49.060.226260.217619X-RAY DIFFRACTION99.3837

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