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- PDB-6izz: The RNA-dependent RNA polymerase domain of dengue 3 NS5, bound wi... -

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Basic information

Entry
Database: PDB / ID: 6izz
TitleThe RNA-dependent RNA polymerase domain of dengue 3 NS5, bound with RK-0404678
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / Dengue / NS5 / RNA-dependent RNA polymerase
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / 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
Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 / Alpha-Beta Plaits / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-oxo-2H-1,3-benzoxathiol-5-yl acetate / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsShimizu, H. / Sekine, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
Japan Society for the Promotion of Science17K07322 Japan
CitationJournal: Plos Negl Trop Dis / Year: 2019
Title: Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase.
Authors: Shimizu, H. / Saito, A. / Mikuni, J. / Nakayama, E.E. / Koyama, H. / Honma, T. / Shirouzu, M. / Sekine, S.I. / Shioda, T.
History
DepositionDec 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1404
Polymers74,7991
Non-polymers3413
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.040, 179.290, 58.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Genome polyprotein


Mass: 74798.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 3 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q5I3C1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-B5C / 2-oxo-2H-1,3-benzoxathiol-5-yl acetate


Mass: 210.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H6O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16% polyethylene glycol 10000 and 100 mM Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→64.67 Å / Num. obs: 60863 / % possible obs: 99.4 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rsym value: 0.089 / Net I/σ(I): 13.8
Reflection shellResolution: 1.97→2.02 Å / Num. unique obs: 4487 / CC1/2: 0.609 / Rsym value: 2.264

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data scaling
Cootmodel building
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J7U

2j7u


Resolution: 1.97→56.153 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 3055 5.03 %
Rwork0.223 --
obs0.2246 60752 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→56.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4615 0 16 331 4962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054742
X-RAY DIFFRACTIONf_angle_d0.7256416
X-RAY DIFFRACTIONf_dihedral_angle_d6.6312831
X-RAY DIFFRACTIONf_chiral_restr0.048675
X-RAY DIFFRACTIONf_plane_restr0.005823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.00080.37931380.37492604X-RAY DIFFRACTION99
2.0008-2.03360.3891390.33292601X-RAY DIFFRACTION100
2.0336-2.06870.481380.48882481X-RAY DIFFRACTION95
2.0687-2.10630.47531240.44932480X-RAY DIFFRACTION95
2.1063-2.14680.29441640.28622573X-RAY DIFFRACTION100
2.1468-2.19060.31441310.28592627X-RAY DIFFRACTION100
2.1906-2.23830.32881450.30712582X-RAY DIFFRACTION98
2.2383-2.29030.52621160.46922555X-RAY DIFFRACTION97
2.2903-2.34760.341370.27972610X-RAY DIFFRACTION100
2.3476-2.41110.22541510.23292614X-RAY DIFFRACTION100
2.4111-2.4820.27671490.22052601X-RAY DIFFRACTION100
2.482-2.56210.22791500.21522614X-RAY DIFFRACTION100
2.5621-2.65370.22161350.20862649X-RAY DIFFRACTION100
2.6537-2.760.25951240.21772652X-RAY DIFFRACTION100
2.76-2.88560.27171340.20642623X-RAY DIFFRACTION100
2.8856-3.03770.25161240.20892662X-RAY DIFFRACTION100
3.0377-3.2280.21761600.19982626X-RAY DIFFRACTION100
3.228-3.47720.23761460.20842644X-RAY DIFFRACTION100
3.4772-3.8270.20581260.18482678X-RAY DIFFRACTION100
3.827-4.38060.22891410.17342670X-RAY DIFFRACTION100
4.3806-5.51840.20921440.18182707X-RAY DIFFRACTION100
5.5184-56.17560.23991390.2022844X-RAY DIFFRACTION100

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