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- PDB-5ikm: 1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Den... -

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Basic information

Entry
Database: PDB / ID: 5ikm
Title1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.
ComponentsNS5 Methyl Transferase
KeywordsTRANSFERASE / NS5 Methyl Transferase / Dengue virus 1 / S-Adenosylmethionine / Beta-D-Fructopyranose / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / 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 capsid protein C superfamily / 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. / 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, flavivirus / Flavivirus envelope glycoprotein M / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-fructopyranose / D-MALATE / S-ADENOSYLMETHIONINE / Core protein
Similarity search - Component
Biological speciesDengue virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Flores, K. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.
Authors: Minasov, G. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Flores, K. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS5 Methyl Transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,91515
Polymers30,2101
Non-polymers1,70514
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-98 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.380, 86.230, 144.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-423-

HOH

31A-577-

HOH

41A-624-

HOH

51A-633-

HOH

61A-678-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein NS5 Methyl Transferase


Mass: 30209.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 1 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: I6XG39
#5: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 295 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 6.8 mg/ml, 0.25M Sodium chloride, 0.1M Tris HCl (pH 8.3); Screen: JCSG+ (E2), 0.2M Sodium chloride, 0.1M Sodium cacodylate (pH 6.5) 2M Ammonium sulfate; Cryo: 4M Ammonium sulfate : 50% Sucrose (1:1).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2014 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 29015 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 17 Å2 / CC1/2: 0.882 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V0Q

4v0q


Resolution: 1.9→29.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.723 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18422 1386 4.8 %RANDOM
Rwork0.15299 ---
obs0.15449 27572 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.827 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2---1.93 Å20 Å2
3---3.06 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 100 282 2435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192371
X-RAY DIFFRACTIONr_bond_other_d0.0010.022236
X-RAY DIFFRACTIONr_angle_refined_deg1.5052.0033223
X-RAY DIFFRACTIONr_angle_other_deg0.86635178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3565296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.19922.55198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5115429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9451522
X-RAY DIFFRACTIONr_chiral_restr0.090.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0212666
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02547
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_it0.640.8071136
X-RAY DIFFRACTIONr_mcbond_other0.6390.8071136
X-RAY DIFFRACTIONr_mcangle_it1.1081.21448
X-RAY DIFFRACTIONr_mcangle_other1.1071.2021449
X-RAY DIFFRACTIONr_scbond_it1.2781.1181233
X-RAY DIFFRACTIONr_scbond_other1.2751.1181233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0521.6221776
X-RAY DIFFRACTIONr_long_range_B_refined7.0798.8442919
X-RAY DIFFRACTIONr_long_range_B_other6.6837.7032772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 107 -
Rwork0.201 2012 -
obs--100 %
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)
14.9626-1.57271.0422.2904-0.08683.07540.14980.3494-0.0935-0.2931-0.10490.00940.1339-0.1301-0.04490.1466-0.03860.01140.14920.00450.005917.001137.93467.0912
20.61320.40320.50215.0988-0.26030.9643-0.02110.0558-0.0323-0.3242-0.0364-0.20370.10190.04050.05750.0580.00540.03720.06550.00240.033623.683523.825126.1017
32.8093-0.54630.60482.47940.0431.9812-0.02390.009-0.05930.00610.04250.0403-0.0153-0.0059-0.01860.08590.00080.00710.06860.01750.032414.710625.710836.0795
41.6414-0.01280.11330.8687-0.53840.915-0.02710.0591-0.00090.00380.01680.0898-0.0609-0.02120.01030.1039-0.00320.00460.1049-0.01190.07136.070937.960930.1972
51.0147-0.1353-0.71950.92020.62131.86670.02230.09130.1032-0.11840.01330.0123-0.0363-0.0032-0.03550.1013-0.01090.00040.10050.01750.040218.885843.43420.4578
61.5794-0.4501-1.93251.1142-1.890610.7061-0.029-0.01030.10820.0297-0.0068-0.0787-0.16640.29010.03580.0406-0.0026-0.00890.05340.01320.060326.521221.676635.9222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 34
2X-RAY DIFFRACTION2A35 - 71
3X-RAY DIFFRACTION3A72 - 127
4X-RAY DIFFRACTION4A128 - 176
5X-RAY DIFFRACTION5A177 - 251
6X-RAY DIFFRACTION6A252 - 264

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