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- PDB-2p41: Crystal Structure of Dengue Methyltransferase in Complex with 7Me... -

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Basic information

Entry
Database: PDB / ID: 2p41
TitleCrystal Structure of Dengue Methyltransferase in Complex with 7MeGpppG2'OMe and S-Adenosyl-L-homocysteine
Componentstype II methyltransferase
KeywordsVIRAL PROTEIN / TRANSFERASE / VIZIER / Viral Enzymes Involved in Replication / Dengue virus methyltransferase / Structural Genomics / Marseilles Structural Genomics Program @ AFMB / MSGP
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid 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 capsid protein C superfamily / 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 capsid protein C superfamily / 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
CITRIC ACID / Chem-G1G / S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsEgloff, M.P. / Marseilles Structural Genomics Program @ AFMB (MSGP)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5
Authors: Egloff, M.P. / Decroly, E. / Malet, H. / Selisko, B. / Benarroch, D. / Ferron, F. / Canard, B.
History
DepositionMar 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: type II methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,74014
Polymers34,3971
Non-polymers2,34313
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: type II methyltransferase
hetero molecules

A: type II methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,48028
Polymers68,7942
Non-polymers4,68526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area8300 Å2
ΔGint-262 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.394, 108.394, 55.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein type II methyltransferase / E.C.2.7.7.48


Mass: 34397.027 Da / Num. of mol.: 1 / Fragment: residues 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Genus: Flavivirus / Species: Dengue virus / Strain: type 2 New Guinea / Gene: NSP5 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS
References: UniProt: Q9WLZ8, UniProt: Q9WLZ5*PLUS, RNA-directed RNA polymerase

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Non-polymers , 6 types, 315 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-G1G / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-GUANOSINE


Mass: 817.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H32N10O18P3
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE DIFFERENCES BETWEEN THIS STRUCTURE AND UNP ENTRY Q9WLZ8_9FLAV REFLECT ACTUAL DIFFERENCES ...SEQUENCE DIFFERENCES BETWEEN THIS STRUCTURE AND UNP ENTRY Q9WLZ8_9FLAV REFLECT ACTUAL DIFFERENCES IN THE cDNA USED FOR EXPRESSION OF THE VIRAL GENE IN E.COLI.

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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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 1.2 M Lithium Sulfate, pH 5.8, VAPOR DIFFUSION, HANGING 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
DetectorDate: Dec 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→38.9 Å / Num. all: 35292 / Num. obs: 35115 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.71 Å2 / Rsym value: 0.034 / Net I/σ(I): 37.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 4976 / Rsym value: 0.215 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L9K

1l9k


Resolution: 1.801→36.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.11 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19588 2070 5.9 %RANDOM
Rwork0.16271 ---
all0.16469 33164 --
obs0.16469 32998 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.058 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.801→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 145 302 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212314
X-RAY DIFFRACTIONr_angle_refined_deg1.5422.0313164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06323.0399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46715391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3661521
X-RAY DIFFRACTIONr_chiral_restr0.1140.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021696
X-RAY DIFFRACTIONr_nbd_refined0.2010.21129
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3850.221
X-RAY DIFFRACTIONr_mcbond_it0.7971.51360
X-RAY DIFFRACTIONr_mcangle_it1.1522149
X-RAY DIFFRACTIONr_scbond_it1.91831110
X-RAY DIFFRACTIONr_scangle_it2.9224.51002
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 141 -
Rwork0.205 2332 -
obs--95.56 %
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)
13.652-0.55390.20986.53991.91473.1704-0.0952-0.33140.04750.32490.163-0.3349-0.0150.0864-0.0678-0.0813-0.0053-0.0383-0.14540.0391-0.1584-5.298176.203628.3873
25.6691-0.4135-1.85424.0096-1.85771.93230.0629-0.07880.1592-0.0544-0.0835-0.3047-0.08520.13780.0206-0.0820.04080.0196-0.1377-0.0261-0.11111.150476.1591.0167
30.5826-0.2217-0.6441.6330.66562.88420.04450.1162-0.0002-0.2719-0.03170.15180.048-0.1976-0.0127-0.1026-0.0009-0.0395-0.1308-0.0065-0.1184-17.263681.64624.698
40.812-0.1473-0.06331.4375-0.03142.43140.0424-0.0031-0.1245-0.0195-0.01820.13190.1588-0.1106-0.0242-0.1378-0.03340.0008-0.1550.003-0.1142-16.827972.82316.6906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 3416 - 43
2X-RAY DIFFRACTION2AA35 - 6044 - 69
3X-RAY DIFFRACTION3AA61 - 17670 - 185
4X-RAY DIFFRACTION4AA177 - 264186 - 273

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