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- PDB-7nxu: Crystal structure of the tick-borne encephalitis virus NS3 helica... -

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Basic information

Entry
Database: PDB / ID: 7nxu
TitleCrystal structure of the tick-borne encephalitis virus NS3 helicase in complex with ADP-Pi
ComponentsNS3 helicase domain
KeywordsVIRAL PROTEIN / RNA helicase / hydrolase / flavivirus
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
ADENOSINE-5'-DIPHOSPHATE / : / PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAnindita, P.D. / Grinkevich, P. / 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
DepositionMar 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Sep 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 1.3Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Jan 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

Downloads & links

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Assembly

Deposited unit
A: NS3 helicase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0895
Polymers53,4891
Non-polymers6004
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-32 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.980, 72.980, 196.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#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: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: A0A2S1PWV0, RNA helicase

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Non-polymers , 5 types, 204 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis Tris Propane, 0.02 M Sodium potassium phosphate pH 7.5, 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: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.097→48.81 Å / Num. obs: 31603 / % possible obs: 99.5 % / Redundancy: 13.67 % / CC1/2: 0.99 / Net I/σ(I): 23.02
Reflection shellResolution: 2.1→2.22 Å / Mean I/σ(I) obs: 3.21 / Num. unique obs: 5033 / CC1/2: 0.904 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BM0

7bm0


Resolution: 2.1→48.806 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.186
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2507 1547 4.896 %
Rwork0.2138 30047 -
all0.216 --
obs-31594 98.396 %
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: 39.018 Å2
Baniso -1Baniso -2Baniso -3
1-1.072 Å2-0 Å2-0 Å2
2--1.072 Å2-0 Å2
3----2.144 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 1 200 3591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133462
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173208
X-RAY DIFFRACTIONr_angle_refined_deg1.541.6534693
X-RAY DIFFRACTIONr_angle_other_deg2.3631.5867370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.535423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91420.503199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71415571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9131536
X-RAY DIFFRACTIONr_chiral_restr0.0760.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023897
X-RAY DIFFRACTIONr_gen_planes_other0.010.02826
X-RAY DIFFRACTIONr_nbd_refined0.2040.2626
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.22950
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21630
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.28
X-RAY DIFFRACTIONr_nbd_other0.3230.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.26
X-RAY DIFFRACTIONr_mcbond_it3.5653.8871704
X-RAY DIFFRACTIONr_mcbond_other3.563.8851703
X-RAY DIFFRACTIONr_mcangle_it5.1115.8182123
X-RAY DIFFRACTIONr_mcangle_other5.115.822124
X-RAY DIFFRACTIONr_scbond_it4.364.4161758
X-RAY DIFFRACTIONr_scbond_other4.3564.4151758
X-RAY DIFFRACTIONr_scangle_it6.7626.452570
X-RAY DIFFRACTIONr_scangle_other6.7616.4592571
X-RAY DIFFRACTIONr_lrange_it7.87344.8433763
X-RAY DIFFRACTIONr_lrange_other7.9544.7733746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1520.3291090.2892207X-RAY DIFFRACTION99.2288
2.152-2.210.3111190.2732135X-RAY DIFFRACTION100
2.21-2.2750.535880.4981678X-RAY DIFFRACTION80.3823
2.275-2.3450.2571050.2492041X-RAY DIFFRACTION99.814
2.345-2.4210.245910.2091980X-RAY DIFFRACTION100
2.421-2.5060.3021020.2121937X-RAY DIFFRACTION100
2.506-2.6010.247930.2091851X-RAY DIFFRACTION100
2.601-2.7070.286940.2421769X-RAY DIFFRACTION98.5714
2.707-2.8280.263780.211709X-RAY DIFFRACTION100
2.828-2.9650.253800.2031659X-RAY DIFFRACTION100
2.965-3.1260.246780.221589X-RAY DIFFRACTION100
3.126-3.3150.23980.231485X-RAY DIFFRACTION100
3.315-3.5440.236860.231377X-RAY DIFFRACTION98.8514
3.544-3.8280.238560.1981332X-RAY DIFFRACTION99.7843
3.828-4.1930.217600.1751212X-RAY DIFFRACTION99.375
4.193-4.6880.192550.1571117X-RAY DIFFRACTION100
4.688-5.4130.217460.1671006X-RAY DIFFRACTION100
5.413-6.6280.231450.19862X-RAY DIFFRACTION99.8899
6.628-9.3680.201400.169686X-RAY DIFFRACTION100

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