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- PDB-3gcz: Yokose virus Methyltransferase in complex with AdoMet -

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Basic information

Entry
Database: PDB / ID: 3gcz
TitleYokose virus Methyltransferase in complex with AdoMet
ComponentsPolyproteinProteolysis
KeywordsTRANSFERASE / Flavivirus / RNA capping / Methyltransferase / viral enzyme structure / ATP-binding / Nucleotide-binding / RNA replication / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / 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 / endoplasmic reticulum membrane / virion membrane / structural molecule activity / extracellular region / ATP binding / metal ion binding / nucleus
Similarity search - Function
Flavivirus non-structural protein NS2B / 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 non-structural protein NS2B / 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
S-ADENOSYLMETHIONINE / Core protein
Similarity search - Component
Biological speciesYokose virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBollati, M. / Milani, M. / Mastrangelo, E. / Bolognesi, M. / Structural Proteomics in Europe (SPINE)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structure of a methyltransferase from a no-known-vector Flavivirus
Authors: Bollati, M. / Milani, M. / Mastrangelo, E. / de Lambellarie, X. / Canard, B. / Bolognesi, M.
History
DepositionFeb 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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

Downloads & links

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Assembly

Deposited unit
A: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6078
Polymers31,6441
Non-polymers9637
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.912, 68.912, 50.806
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Polyprotein / Proteolysis / NS5 methyltransferase


Mass: 31644.389 Da / Num. of mol.: 1
Fragment: NS5 N-terminal methyltransferase domain, UNP residues 2520-2784
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yokose virus / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q7T918, methyltransferase cap1
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE SEQUENCING ANALYSIS (BMR SEQUENCING SERVICE, UNIVERSITY OF PADOVA, ITALY) SHOWED THAT DURING ...THE SEQUENCING ANALYSIS (BMR SEQUENCING SERVICE, UNIVERSITY OF PADOVA, ITALY) SHOWED THAT DURING THE PCR TWO MUTATIONS OCCURS WITHIN THE YVMTASESC SEQUENCE: K46E AND K163R.

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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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2% PEG 400, 1.5M ammonium sulphate, 100mM HEPES-Na pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 26, 2007
RadiationMonochromator: Diamond / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→51 Å / Num. all: 30809 / Num. obs: 29342 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Net I/σ(I): 24.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3984 / % possible all: 91.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
REFMAC5.5.0066refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R6A

1r6a


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.979 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1477 5 %RANDOM
Rwork0.16705 ---
obs0.16863 27820 98.67 %-
all-29211 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 60 157 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222150
X-RAY DIFFRACTIONr_bond_other_d00.021984
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9942905
X-RAY DIFFRACTIONr_angle_other_deg1.43334620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2035260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99223.40791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05615391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1431519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.51291
X-RAY DIFFRACTIONr_mcbond_other0.1971.5537
X-RAY DIFFRACTIONr_mcangle_it1.3122091
X-RAY DIFFRACTIONr_scbond_it1.9863859
X-RAY DIFFRACTIONr_scangle_it3.1884.5813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 110 -
Rwork0.231 1819 -
obs--87.29 %
Refinement TLS params.Method: refined / Origin x: -15.0296 Å / Origin y: 16.6917 Å / Origin z: 0.9164 Å
111213212223313233
T0.0034 Å20.0028 Å20.0051 Å2-0.0078 Å20.0021 Å2--0.0104 Å2
L0.7141 °2-0.087 °2-0.0469 °2-0.6586 °20.4741 °2--0.9628 °2
S0.0063 Å °-0.0365 Å °0.0374 Å °-0.0242 Å °0.0187 Å °-0.0519 Å °-0.0293 Å °0.0067 Å °-0.025 Å °

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