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- PDB-3eld: Wesselsbron methyltransferase in complex with Sinefungin -

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Basic information

Entry
Database: PDB / ID: 3eld
TitleWesselsbron methyltransferase in complex with Sinefungin
ComponentsMethyltransferase
KeywordsTRANSFERASE / Flavivirus / RNA capping / Methyltransferase / Guanylyltransferase / viral enzyme structure
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / helicase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / helicase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / 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 / 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. ...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 / Vaccinia Virus protein VP39 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Genome polyprotein / Methyltransferase
Similarity search - Component
Biological speciesWesselsbron virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBollati, M. / Milani, M. / Mastrangelo, E. / Ricagno, S. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Recognition of RNA Cap in the Wesselsbron Virus NS5 Methyltransferase Domain: Implications for RNA-Capping Mechanisms in Flavivirus
Authors: Bollati, M. / Milani, M. / Mastrangelo, E. / Ricagno, S. / Tedeschi, G. / Nonnis, S. / Decroly, E. / Selisko, B. / de Lamballerie, X. / Coutard, B. / Canard, B. / Bolognesi, M.
History
DepositionSep 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6713
Polymers34,1931
Non-polymers4772
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.670, 66.132, 88.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methyltransferase


Mass: 34193.172 Da / Num. of mol.: 1
Fragment: NS5 N-terminal methyltransferase domain, UNP residues 2500-2791
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wesselsbron virus / Strain: SAH-177 99871-2 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) PROS
References: UniProt: C8XPB0, UniProt: D0VX01*PLUS, methyltransferase cap1
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2mM Sinefungin, 20% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2007 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→44.24 Å / Num. all: 23718 / Num. obs: 22589 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / Num. unique all: 3224 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3elu

3elu


Resolution: 1.9→38.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.358 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22431 1130 5 %RANDOM
Rwork0.17606 ---
all0.17849 22494 --
obs0.17849 21423 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 32 282 2533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222293
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9683093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8255275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62422.19105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06715415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.551526
X-RAY DIFFRACTIONr_chiral_restr0.0670.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021703
X-RAY DIFFRACTIONr_nbd_refined0.1820.21041
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.219
X-RAY DIFFRACTIONr_mcbond_it1.78521419
X-RAY DIFFRACTIONr_mcangle_it2.35532219
X-RAY DIFFRACTIONr_scbond_it3.91741000
X-RAY DIFFRACTIONr_scangle_it5.7826874
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 68 -
Rwork0.254 1546 -
obs--99.14 %

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