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- PDB-7jno: X-ray crystallographic structure of the NS3 helicase domain from ... -

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Basic information

Entry
Database: PDB / ID: 7jno
TitleX-ray crystallographic structure of the NS3 helicase domain from Tick-borne encephalitis virus
ComponentsSerine protease NS3
KeywordsVIRAL PROTEIN / HYDROLASE / Helicase
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / molecular replacement / Resolution: 1.95 Å
AuthorsWeeks, S.D. / Munwar, A. / Lucero, H.A. / Bandara, A. / Munawar, A.H.
CitationJournal: To Be Published
Title: Crystal structure of Tickborne Encephalitis Virus NS3-Helicase and implications for drug design
Authors: Weeks, S.D. / Fahem, S. / Bandara, A. / Munwar, A. / Lucero, H.A. / Munawar, A.H.
History
DepositionAug 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)49,3221
Polymers49,3221
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.787, 55.442, 91.267
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine protease NS3 / NS3 RNA helicase


Mass: 49321.531 Da / Num. of mol.: 1 / Fragment: Helicase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus / Strain: Hypr / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q01299, RNA helicase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystals were initially identified in the Morpheus II screen condition G5 (15% PEG 3K, 20% 1,2,4 butanetriol, 1% NDSB-256, 20 mM arginine, 20 mM threonine, 20 mM histidine, 20 mM ...Details: Crystals were initially identified in the Morpheus II screen condition G5 (15% PEG 3K, 20% 1,2,4 butanetriol, 1% NDSB-256, 20 mM arginine, 20 mM threonine, 20 mM histidine, 20 mM hydroxylysine, 20 mM trans-4-hydroxy-L-proline, and buffered by 50 mM BES and 50 mM triethanolamine at pH 7.5). Seeds were generated from this condition and used for random microseed matrix screening (rMMS) using a protein concentration of 10-12 mg/ml. Final crystals were identified in the Index HT screen condition H2 (0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350). Crystals were cryoprotected by transfer to a drop containing a 4:1 ratio of precipitant ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920089 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 6, 2019
RadiationMonochromator: Double Crystal Monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920089 Å / Relative weight: 1
ReflectionResolution: 1.95→45.55 Å / Num. obs: 31169 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.053 / Rrim(I) all: 0.135 / Net I/σ(I): 7.7 / Num. measured all: 190446 / Scaling rejects: 1730
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-24.20.28892221170.4530.1620.3272.793.7
8.72-45.556.70.06425403780.9960.0260.06913.699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
xia20.6.467-geb301d90-dials-2.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJC

5gjc


Resolution: 1.95→45.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.227 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1523 4.9 %RANDOM
Rwork0.1821 ---
obs0.1841 29614 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.37 Å2 / Biso mean: 26.02 Å2 / Biso min: 13.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å2-0 Å21.36 Å2
2---2.97 Å20 Å2
3---1.62 Å2
Refinement stepCycle: final / Resolution: 1.95→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 184 3530
Biso mean---30.88 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133441
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173153
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6524670
X-RAY DIFFRACTIONr_angle_other_deg1.3711.5827273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7515429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.3620.251199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28115569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7391537
X-RAY DIFFRACTIONr_chiral_restr0.0790.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 120 -
Rwork0.21 1998 -
all-2118 -
obs--93.39 %
Refinement TLS params.Method: refined / Origin x: 11.418 Å / Origin y: 7.42 Å / Origin z: 22.113 Å
111213212223313233
T0.0232 Å2-0.031 Å20.0097 Å2-0.1183 Å2-0.0221 Å2--0.0114 Å2
L0.8332 °2-0.1093 °2-0.6059 °2-1.5447 °2-0.2286 °2--1.2952 °2
S0.0131 Å °-0.0485 Å °-0.0478 Å °0.0326 Å °-0.0153 Å °0.0222 Å °0.0334 Å °0.1057 Å °0.0023 Å °

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