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- PDB-3emd: Wesselsbron virus Methyltransferase in complex with Sinefungin an... -

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Basic information

Entry
Database: PDB / ID: 3emd
TitleWesselsbron virus Methyltransferase in complex with Sinefungin and 7MeGpppA
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
Chem-GTA / SINEFUNGIN / Genome polyprotein / Methyltransferase
Similarity search - Component
Biological speciesWesselsbron virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBollati, M. / Milani, M. / Ricagno, S. / Mastrangelo, E. / 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 24, 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)35,6506
Polymers34,1931
Non-polymers1,4575
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.057, 61.157, 128.831
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-GTA / P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / 7-METHYL-GPPPA


Mass: 787.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O17P3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE THIRD PHOSPHATE GROUP IS NOT VISIBLE IN THE STRUCTURE AS WELL AS THE ADENOSINE.

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 1mM Sinefungin, 1mM 7MeGpppA, 10% PEG 4000, pH 6.2, 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: Nov 10, 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: 2→44.37 Å / Num. all: 21485 / Num. obs: 20462 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3093 / % possible all: 99.9

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Processing

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

3elu


Resolution: 2→32.21 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.172 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21466 1045 5.1 %RANDOM
Rwork0.16189 ---
all0.16457 20333 --
obs0.16457 19365 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.475 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 71 317 2470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212217
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9883002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1575262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9621.881101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21315394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0551526
X-RAY DIFFRACTIONr_chiral_restr0.0740.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021644
X-RAY DIFFRACTIONr_nbd_refined0.1820.21046
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.225
X-RAY DIFFRACTIONr_mcbond_it1.31521294
X-RAY DIFFRACTIONr_mcangle_it2.21332095
X-RAY DIFFRACTIONr_scbond_it3.484923
X-RAY DIFFRACTIONr_scangle_it5.1336906
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 69 -
Rwork0.178 1437 -
obs--99.87 %

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