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- PDB-8qdj: Ntaya virus methyltransferase in complex wih Sinefungin -

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Basic information

Entry
Database: PDB / ID: 8qdj
TitleNtaya virus methyltransferase in complex wih Sinefungin
ComponentsNtaya virus methyltransferase
KeywordsVIRAL PROTEIN / flavivirus / ntaya virus / sinefungin / methyltransferase
Function / homology
Function and homology information


: / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 innate immune response ...: / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 innate immune response / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / GTP binding / 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SINEFUNGIN / Genome polyprotein
Similarity search - Component
Biological speciesNtaya virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKrejcova, K. / Boura, E. / Klima, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Not funded Czech Republic
CitationJournal: Structure / Year: 2024
Title: Structural and functional insights in flavivirus NS5 proteins gained by the structure of Ntaya virus polymerase and methyltransferase.
Authors: Krejcova, K. / Krafcikova, P. / Klima, M. / Chalupska, D. / Chalupsky, K. / Zilecka, E. / Boura, E.
History
DepositionAug 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ntaya virus methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0453
Polymers29,5681
Non-polymers4772
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.389, 71.092, 50.445
Angle α, β, γ (deg.)90.000, 92.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Ntaya virus methyltransferase / Ntaya virus methyltransferase


Mass: 29567.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ntaya virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K0BRZ6
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Bis-Tri 5.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→26.07 Å / Num. obs: 25149 / % possible obs: 99.85 % / Redundancy: 2 % / Biso Wilson estimate: 13.27 Å2 / CC1/2: 0.878 / Rmerge(I) obs: 0.1991 / Rpim(I) all: 0.1991 / Rrim(I) all: 0.2815 / Net I/σ(I): 16.35
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 2 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 2492 / CC1/2: 0.79 / CC star: 0.939 / Rpim(I) all: 0.335 / Rrim(I) all: 0.4737 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→26.07 Å / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.7411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2086 1990 7.92 %
Rwork0.1729 23133 -
obs0.1757 25123 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 32 240 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582114
X-RAY DIFFRACTIONf_angle_d0.77032856
X-RAY DIFFRACTIONf_chiral_restr0.0493303
X-RAY DIFFRACTIONf_plane_restr0.0084372
X-RAY DIFFRACTIONf_dihedral_angle_d12.4032806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.27491420.22791631X-RAY DIFFRACTION99.94
1.85-1.890.26711330.2081651X-RAY DIFFRACTION100
1.89-1.950.23241560.18871631X-RAY DIFFRACTION100
1.95-2.010.26631360.18581676X-RAY DIFFRACTION100
2.01-2.090.22251360.17741614X-RAY DIFFRACTION98.81
2.09-2.170.241400.17171645X-RAY DIFFRACTION100
2.17-2.270.19641430.16511646X-RAY DIFFRACTION100
2.27-2.390.24711420.17091667X-RAY DIFFRACTION100
2.39-2.540.1951360.17531654X-RAY DIFFRACTION100
2.54-2.730.23131440.18231661X-RAY DIFFRACTION100
2.73-3.010.23451410.18721654X-RAY DIFFRACTION100
3.01-3.440.19661530.1711641X-RAY DIFFRACTION99.94
3.44-4.330.16691410.14861664X-RAY DIFFRACTION99.94
4.33-26.070.15671470.15711698X-RAY DIFFRACTION99.89

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