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- PDB-5xc6: Dengue Virus 4 NS3 Helicase in complex with SSRNA SLA12 -

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Basic information

Entry
Database: PDB / ID: 5xc6
TitleDengue Virus 4 NS3 Helicase in complex with SSRNA SLA12
Components
  • NS3 Helicase
  • RNA (5'-R(*AP*GP*UP*UP*GP*UP*UP*AP*GP*UP*CP*U)-3')
KeywordsHYDROLASE/RNA / Helicase / Dengue NS3 / RNA / Hydrolase / HYDROLASE-RNA complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / 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 / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / 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 superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / 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 / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 4
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSwarbrick, C.M.D. / Basavannacharya, C. / Chan, K.W.K. / Chan, S.A. / Singh, D. / Wei, N. / Phoo, W.W. / Luo, D. / Lescar, J. / Vasudevan, S.G.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication
Authors: Swarbrick, C.M.D. / Basavannacharya, C. / Chan, K.W.K. / Chan, S.A. / Singh, D. / Wei, N. / Phoo, W.W. / Luo, D. / Lescar, J. / Vasudevan, S.G.
History
DepositionMar 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.3Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: NS3 Helicase
B: NS3 Helicase
C: RNA (5'-R(*AP*GP*UP*UP*GP*UP*UP*AP*GP*UP*CP*U)-3')
D: RNA (5'-R(*AP*GP*UP*UP*GP*UP*UP*AP*GP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5036
Polymers110,3144
Non-polymers1902
Water0
1
A: NS3 Helicase
C: RNA (5'-R(*AP*GP*UP*UP*GP*UP*UP*AP*GP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2523
Polymers55,1572
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-22 kcal/mol
Surface area20930 Å2
MethodPISA
2
B: NS3 Helicase
D: RNA (5'-R(*AP*GP*UP*UP*GP*UP*UP*AP*GP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2523
Polymers55,1572
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-23 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.899, 105.406, 72.694
Angle α, β, γ (deg.)90.00, 116.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NS3 Helicase


Mass: 51365.527 Da / Num. of mol.: 2 / Fragment: UNP residues 1646-2092 / Mutation: E250D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Strain: Thailand/0348/1991 / Production host: Escherichia coli (E. coli) / References: UniProt: M9P7S0
#2: RNA chain RNA (5'-R(*AP*GP*UP*UP*GP*UP*UP*AP*GP*UP*CP*U)-3')


Mass: 3791.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 15% polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.9→19.86 Å / Num. obs: 19928 / % possible obs: 99.7 % / Redundancy: 3.6 % / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JLU

2jlu


Resolution: 2.9→19.859 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 1017 5.1 %
Rwork0.2014 --
obs0.2042 19928 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→19.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7218 216 10 0 7444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097614
X-RAY DIFFRACTIONf_angle_d1.22510361
X-RAY DIFFRACTIONf_dihedral_angle_d24.1442939
X-RAY DIFFRACTIONf_chiral_restr0.2311132
X-RAY DIFFRACTIONf_plane_restr0.0071319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.05250.36431430.30092672X-RAY DIFFRACTION100
3.0525-3.2430.32761290.2722719X-RAY DIFFRACTION100
3.243-3.49210.26911690.23432663X-RAY DIFFRACTION100
3.4921-3.84120.27991350.20542700X-RAY DIFFRACTION100
3.8412-4.39180.23431510.17332690X-RAY DIFFRACTION100
4.3918-5.51360.22841370.16442721X-RAY DIFFRACTION100
5.5136-19.85950.20231530.1692746X-RAY DIFFRACTION100

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