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- PDB-8zmc: Dengue 3 NS5 methyltransferase bound to S-Adenosyl-L-homocysteine... -

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Basic information

Entry
Database: PDB / ID: 8zmc
TitleDengue 3 NS5 methyltransferase bound to S-Adenosyl-L-homocysteine and Herbacetin
ComponentsDengue 3 NS5 methyltransferase
KeywordsTRANSFERASE / Dengue virus 3 NS5 Methyltransferase
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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein
Similarity search - Component
Biological speciesdengue virus type 3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBhutkar, M. / Verma, S. / Tomar, S. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchISRM/12(46)/2020 India
CitationJournal: To Be Published
Title: Dengue 3 NS5 methyltransferase bound to S-Adenosyl-L-homocysteine and Herbacetin
Authors: Bhutkar, M. / Verma, S. / Tomar, S. / Kumar, P.
History
DepositionMay 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dengue 3 NS5 methyltransferase
B: Dengue 3 NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,63110
Polymers64,1002
Non-polymers1,5328
Water00
1
A: Dengue 3 NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1057
Polymers32,0501
Non-polymers1,0556
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dengue 3 NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5263
Polymers32,0501
Non-polymers4772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.877, 59.966, 185.044
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 7 - 262 / Label seq-ID: 26 - 281

Dom-ID
1
2

NCS ensembles : (Details: Global NCS restraints between domains: 1 2)

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Components

#1: Protein Dengue 3 NS5 methyltransferase / Genome polyprotein


Mass: 32049.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) dengue virus type 3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1KBQ3, EC: 2.1.1.358
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-A1L1Z / Herbacetin / 2-(4-hydroxyphenyl)-3,5,7,8-tetrakis(oxidanyl)chromen-4-one


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 8000 100 mM Tris 200 mM NaCl 20 mM Trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.8→24.892 Å / Num. obs: 20387 / % possible obs: 99.9 % / Redundancy: 19.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.8
Reflection shellResolution: 2.8→2.95 Å / Mean I/σ(I) obs: 4.6 / Num. unique obs: 20387 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R8R

4r8r


Resolution: 2.8→24.892 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.809 / SU B: 42 / SU ML: 0.441 / Cross valid method: FREE R-VALUE / ESU R Free: 0.473 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.3025 707 4.847 %
Rwork0.2589 13879 -
all0.261 --
obs-14586 99.679 %
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: 36.984 Å2
Baniso -1Baniso -2Baniso -3
1--4.265 Å2-0 Å2-0 Å2
2---4.401 Å2-0 Å2
3---8.666 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 104 0 4182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124271
X-RAY DIFFRACTIONr_ext_dist_refined_b0.0470.170325
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.8625757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4295510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.2855.78938
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00610784
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.93410178
X-RAY DIFFRACTIONr_chiral_restr0.0980.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023190
X-RAY DIFFRACTIONr_nbd_refined0.2210.21869
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5920.25
X-RAY DIFFRACTIONr_mcbond_it1.452.1162052
X-RAY DIFFRACTIONr_mcangle_it2.4543.7992558
X-RAY DIFFRACTIONr_scbond_it2.1822.332219
X-RAY DIFFRACTIONr_scangle_it3.4544.1823199
X-RAY DIFFRACTIONr_lrange_it6.86946.95971342
Refine LS restraints NCS

Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Rms dev Biso : 6.97333 Å2 / Rms dev position: 0.11997 Å / Weight Biso : 0.5 / Weight position: 0.05

Dom-ID
1
2
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8720.351490.3451000X-RAY DIFFRACTION100
2.872-2.9490.393410.321965X-RAY DIFFRACTION100
2.949-3.0340.352590.312950X-RAY DIFFRACTION100
3.034-3.1260.311400.299909X-RAY DIFFRACTION99.8947
3.126-3.2260.343390.288893X-RAY DIFFRACTION100
3.226-3.3380.338460.292880X-RAY DIFFRACTION100
3.338-3.4610.393520.278811X-RAY DIFFRACTION99.8843
3.461-3.60.332470.27815X-RAY DIFFRACTION99.8841
3.6-3.7560.26480.252765X-RAY DIFFRACTION99.8772
3.756-3.9350.258340.237761X-RAY DIFFRACTION99.7491
3.935-4.1420.294370.237697X-RAY DIFFRACTION100
4.142-4.3860.247320.234683X-RAY DIFFRACTION99.8603
4.386-4.6780.261360.23645X-RAY DIFFRACTION99.2711
4.678-5.0380.256280.223599X-RAY DIFFRACTION99.8408
5.038-5.4970.281270.249555X-RAY DIFFRACTION99.4872
5.497-6.1080.301270.274512X-RAY DIFFRACTION100
6.108-6.9840.253250.245456X-RAY DIFFRACTION100
6.984-8.390.293140.2417X-RAY DIFFRACTION100
8-100.229170.172328X-RAY DIFFRACTION100
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)Origin x (Å)Origin y (Å)Origin z (Å)
10.5113-0.0706-0.21991.24290.02340.40010.02010.0357-0.0368-0.05140.0245-0.02210.00490.0277-0.04460.07970.0110.08010.10080.00220.15651.6335-9.813341.6425
21.85620.16490.39121.3304-1.09981.1328-0.09960.13680.0458-0.01290.12660.04240.0688-0.0567-0.0270.1547-0.02550.04230.15590.00770.036411.644916.058413.0185
Refinement TLS groupSelection: ALL

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