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- PDB-5ehg: DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-ADENOSYL METHIONINE AND... -

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Basic information

Entry
Database: PDB / ID: 5ehg
TitleDENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-ADENOSYL METHIONINE AND MOLECULE BF341
ComponentsRNA-directed RNA polymerase NS5
KeywordsTRANSFERASE / DENGUE VIRUS / NS5 METHYLTRANSFERASE / FRAGMENT-BASED DRUG DISCOVERY
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / 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 / Vaccinia Virus protein VP39 / 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, 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
Chem-5O0 / S-ADENOSYLMETHIONINE / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus type 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsBarral, K. / Bricogne, G. / Sharff, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR- 13-JS07-0006-01 France
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Discovery of novel dengue virus NS5 methyltransferase non-nucleoside inhibitors by fragment-based drug design.
Authors: Benmansour, F. / Trist, I. / Coutard, B. / Decroly, E. / Querat, G. / Brancale, A. / Barral, K.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Refinement description
Category: diffrn_radiation_wavelength / pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase NS5
C: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6725
Polymers62,4142
Non-polymers1,2593
Water7,638424
1
A: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0673
Polymers31,2071
Non-polymers8602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6052
Polymers31,2071
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.145, 185.730, 52.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RNA-directed RNA polymerase NS5


Mass: 31206.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: synthetic gene
Source: (gene. exp.) Dengue virus type 3 (strain Philippines/H87/1956)
Strain: Philippines/H87/1956 / Plasmid: PMCOX20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): Rosetta
References: UniProt: P27915, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-5O0 / 4-[3-[(2-azanyl-4-chloranyl-phenyl)carbamoylamino]phenyl]sulfonyloxybenzoic acid


Mass: 461.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16ClN3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 8000 100mM Tris 200mM NaCl 20mM Trisodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.015→92.86 Å / Num. obs: 39664 / % possible obs: 98.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.57 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 9.5
Reflection shellResolution: 2.015→2.022 Å / Redundancy: 4 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.967 / % possible all: 99.7

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Processing

Software
NameVersionClassification
autoPROCdata collection
XDS(VERSION January 10data reduction
PDB_EXTRACT(version 0.3.11)data extraction
SCALA6.4data scaling
BUSTER2.10.2refinement
PHASERphasing
Aimless(version 0.3.11)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P97

3p97


Resolution: 2.02→92.86 Å / Cor.coef. Fo:Fc: 0.9168 / Cor.coef. Fo:Fc free: 0.8862 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.178 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 2061 5.24 %RANDOM
Rwork0.1704 ---
obs0.1734 39360 98.7 %-
Displacement parametersBiso mean: 25.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.6649 Å20 Å20 Å2
2---11.4824 Å20 Å2
3---9.8175 Å2
Refine analyzeLuzzati coordinate error obs: 0.229 Å
Refinement stepCycle: LAST / Resolution: 2.02→92.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 85 424 4588
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014303HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035816HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1563SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes670HARMONIC5
X-RAY DIFFRACTIONt_it4303HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion16.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion536SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5093SEMIHARMONIC4
LS refinement shellResolution: 2.02→2.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2849 145 5.04 %
Rwork0.1919 2730 -
all0.1966 2875 -
obs--98.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.92230.23930.08860.50270.18570.95750.0170.0587-0.03210.0150.01240.00010.05210.0517-0.0294-0.11210.0091-0.00340.018-0.0036-0.0212chain A39.935841.7815-1.7245
21.08190.27640.73290.9644-0.33693.42530.17290.0809-0.1011-0.019-0.01710.02730.46160.0859-0.1557-0.02160.0056-0.0372-0.1676-0.0328-0.0718chain C14.035713.0666-10.7327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|* }C7 - 262
2X-RAY DIFFRACTION2{ C|* }

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