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- PDB-5m5b: Crystal structure of Zika virus NS5 methyltransferase -

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Basic information

Entry
Database: PDB / ID: 5m5b
TitleCrystal structure of Zika virus NS5 methyltransferase
ComponentsNS5 methyltransferase
KeywordsTRANSFERASE / Zika virus NS5 methyltransferase
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / molecular adaptor activity / clathrin-dependent endocytosis of virus by host cell / host cell surface / 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 / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / centrosome / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 / 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 / DNA/RNA polymerase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsBarral, K. / Ortiz Lombardia, M. / Coutard, B. / Decroly, E. / Lichiere, J.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR- 13-JS07-0006-01 France
CitationJournal: J. Virol. / Year: 2017
Title: Zika Virus Methyltransferase: Structure and Functions for Drug Design Perspectives.
Authors: Coutard, B. / Barral, K. / Lichiere, J. / Selisko, B. / Martin, B. / Aouadi, W. / Lombardia, M.O. / Debart, F. / Vasseur, J.J. / Guillemot, J.C. / Canard, B. / Decroly, E.
History
DepositionOct 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS5 methyltransferase
B: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6229
Polymers60,7112
Non-polymers9107
Water6,864381
1
A: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9464
Polymers30,3561
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6755
Polymers30,3561
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.550, 64.140, 72.040
Angle α, β, γ (deg.)113.05, 97.78, 92.00
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NS5 methyltransferase


Mass: 30355.740 Da / Num. of mol.: 2 / Fragment: UNP residues 2525-2786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Plasmid: pQE30 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): T7 express Iq / References: UniProt: H9A910, UniProt: A0A024B7W1*PLUS

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Non-polymers , 5 types, 388 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 150 mM sodium citrate 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98009 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 2.01→65.41 Å / Num. obs: 40055 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.23 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.083 / Rrim(I) all: 0.157 / Net I/σ(I): 5.8
Reflection shellResolution: 2.015→2.022 Å / Rmerge(I) obs: 0.359 / Rpim(I) all: 0.272 / Rrim(I) all: 0.454

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata collection
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P97

3p97


Resolution: 2.01→65.41 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2105 5.26 %RANDOM
Rwork0.16 ---
obs0.162 40054 98.6 %-
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.9028 Å2-6.4769 Å22.9982 Å2
2---0.4706 Å21.2358 Å2
3---3.3734 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 2.01→65.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 54 381 4388
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014179HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965655HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1498SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes633HARMONIC5
X-RAY DIFFRACTIONt_it4179HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion16.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5027SEMIHARMONIC4
LS refinement shellResolution: 2.01→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 146 5.52 %
Rwork0.201 2501 -
all0.203 2647 -
obs--87.01 %
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)
11.4136-0.83750.68171.8032-0.50840.871-0.0063-0.0756-0.0437-0.02720.0388-0.00630.136-0.013-0.0325-0.0902-0.00560.0022-0.0355-0.0099-0.07832.733435.631486.128
20.9778-0.22030.24830.8569-0.13642.30070.00460.041-0.0022-0.0149-0.0784-0.021-0.10420.05660.0738-0.06370.0209-0.0026-0.06660.0044-0.071-6.59615.647262.3222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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