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

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Basic information

Entry
Database: PDB / ID: 7blv
TitleCrystal structure of the tick-borne encephalitis virus NS3 helicase in complex with ADP
ComponentsNS3 helicase domain
KeywordsVIRAL PROTEIN / RNA helicase / hydrolase
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 / : / Genome polyprotein
Similarity search - Component
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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
DepositionJan 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 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

Downloads & links

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Assembly

Deposited unit
A: NS3 helicase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9713
Polymers53,4891
Non-polymers4822
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-13 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.120, 73.120, 196.124
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 BL21 (bacteria) / Variant (production host): Codonplus-RIPL / References: UniProt: A0A2S1PWV0, RNA helicase
#2: 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
#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: 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis Tris Propane pH 6.5, 0.2 M sodium acetate truhydrate, 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 PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 32056 / % possible obs: 99.9 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rrim(I) all: 0.067 / Net I/σ(I): 24.38
Reflection shellResolution: 2.099→2.23 Å / Mean I/σ(I) obs: 2.53 / Num. unique obs: 5054 / CC1/2: 0.839 / Rrim(I) all: 0.99 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AY4

7ay4
PDB Unreleased entry


Resolution: 2.099→45.778 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.226 / SU B: 5.825 / SU ML: 0.15 / Average fsc free: 0.8804 / Average fsc work: 0.886 / Cross valid method: FREE R-VALUE / ESU R: 0.228 / ESU R Free: 0.187 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.259 1565 4.882 %
Rwork0.2329 30491 -
all0.234 --
obs-32056 99.888 %
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: 57.908 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å2-0 Å2-0 Å2
2--1.42 Å20 Å2
3----2.839 Å2
Refinement stepCycle: LAST / Resolution: 2.099→45.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 1 75 3490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123489
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.6494729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.275423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02520.191209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53315592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0241540
X-RAY DIFFRACTIONr_chiral_restr0.1110.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022676
X-RAY DIFFRACTIONr_nbd_refined0.2140.21463
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.26
X-RAY DIFFRACTIONr_mcbond_it5.0495.5571701
X-RAY DIFFRACTIONr_mcangle_it6.7698.3012121
X-RAY DIFFRACTIONr_scbond_it5.6375.9721788
X-RAY DIFFRACTIONr_scangle_it7.9518.7462608
X-RAY DIFFRACTIONr_lrange_it9.81572.9255071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.099-2.1530.3441050.3442219X-RAY DIFFRACTION99.2738
2.153-2.2120.3031210.3032137X-RAY DIFFRACTION100
2.212-2.2760.3051080.3052082X-RAY DIFFRACTION99.9544
2.276-2.3460.2981010.282040X-RAY DIFFRACTION100
2.346-2.4230.289920.2761972X-RAY DIFFRACTION99.9032
2.423-2.5080.3241030.2771937X-RAY DIFFRACTION99.951
2.508-2.6030.29920.2681866X-RAY DIFFRACTION99.949
2.603-2.7090.345970.251777X-RAY DIFFRACTION99.8934
2.709-2.830.274780.2681716X-RAY DIFFRACTION99.9443
2.83-2.9680.307780.2721657X-RAY DIFFRACTION100
2.968-3.1280.262800.2621574X-RAY DIFFRACTION100
3.128-3.3180.293970.2571489X-RAY DIFFRACTION100
3.318-3.5470.266860.2661393X-RAY DIFFRACTION100
3.547-3.8310.282570.2461331X-RAY DIFFRACTION100
3.831-4.1960.226600.1941219X-RAY DIFFRACTION100
4.196-4.6920.186550.1781118X-RAY DIFFRACTION99.9148
4.692-5.4170.212460.1781006X-RAY DIFFRACTION100
5.417-6.6330.246450.199861X-RAY DIFFRACTION99.8897
6.633-9.3750.208400.171686X-RAY DIFFRACTION100

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