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- PDB-5kqs: Structure of NS5 methyltransferase from Zika virus bound to S-ade... -

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Basic information

Entry
Database: PDB / ID: 5kqs
TitleStructure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and 7-methyl-guanosine-5'-diphosphate
ComponentsMethyltransferase
KeywordsTRANSFERASE / Zika / Flavivirus / Methyltransferase / NS5
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / host cell surface / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / molecular adaptor activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / centrosome / viral envelope / lipid binding / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / S-ADENOSYLMETHIONINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsColoma, J. / Jain, R. / Rajashankar, K.R. / Aggarwal, A.K.
CitationJournal: Cell Rep / Year: 2016
Title: Structures of NS5 Methyltransferase from Zika Virus.
Authors: Coloma, J. / Jain, R. / Rajashankar, K.R. / Garcia-Sastre, A. / Aggarwal, A.K.
History
DepositionJul 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Aug 3, 2022Group: Database references / Structure summary / Category: database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)30,9199
Polymers29,5391
Non-polymers1,3808
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.340, 77.480, 37.030
Angle α, β, γ (deg.)90.000, 104.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase


Mass: 29538.742 Da / Num. of mol.: 1 / Fragment: MRNA cap 0-1 NS5-type MT residues 2521-2786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: H9A910, UniProt: A0A024B7W1*PLUS

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Non-polymers , 6 types, 252 molecules

#2: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 459.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O11P2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 6-9 % PEG 8K, 0.07 M Sodium acetate, pH 5.0, 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→65.9 Å / Num. obs: 56456 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.29 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.043 / Rrim(I) all: 0.082 / Net I/σ(I): 7.6 / Num. measured all: 184856 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.5-1.533.30.813917727620.6090.5120.9651.3
8.22-65.93.80.04714003710.9960.0260.05416.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
MOSFLMdata reduction
Aimless0.5.12data scaling
PDB_EXTRACT3.2data extraction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PX2

2px2


Resolution: 1.5→38.74 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1788 2847 5.08 %
Rwork0.1585 53204 -
obs0.1595 56051 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.76 Å2 / Biso mean: 30.1534 Å2 / Biso min: 13.48 Å2
Refinement stepCycle: final / Resolution: 1.5→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 118 244 2347
Biso mean--37.68 44.1 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052178
X-RAY DIFFRACTIONf_angle_d0.8612956
X-RAY DIFFRACTIONf_chiral_restr0.074314
X-RAY DIFFRACTIONf_plane_restr0.005363
X-RAY DIFFRACTIONf_dihedral_angle_d27.824800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52590.30681320.28492582271497
1.5259-1.55360.25331340.25272657279198
1.5536-1.58350.21121390.21662625276499
1.5835-1.61580.24891470.20532653280098
1.6158-1.65090.2291610.19422622278399
1.6509-1.68940.23121430.18622629277299
1.6894-1.73160.20141470.17162636278399
1.7316-1.77840.18741610.16772659282099
1.7784-1.83070.21471370.16132655279299
1.8307-1.88980.19431160.15962656277299
1.8898-1.95740.17831460.15992679282599
1.9574-2.03570.18271370.15252662279999
2.0357-2.12840.17731460.15732642278899
2.1284-2.24060.16851550.149126472802100
2.2406-2.3810.16571350.15252693282899
2.381-2.56480.17511420.157226772819100
2.5648-2.82280.18961220.164827262848100
2.8228-3.23110.17241380.162686282499
3.2311-4.07010.16091440.13627092853100
4.0701-38.75310.1651650.15092709287499
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)
14.5746-0.4513-0.6050.918-0.30433.01280.18250.04720.67360.1309-0.1194-0.5061-0.12450.22820.00760.1646-0.0349-0.02110.17520.02070.415454.771214.95033.1016
23.30711.14540.11591.5867-0.07271.5118-0.11480.3856-0.49630.03820.1082-0.51480.30810.2209-0.14590.28660.0189-0.01870.2668-0.02940.329748.3248-8.98835.7856
34.6674-0.19070.33721.8374-1.16676.02190.01090.0011-0.15470.01240.067-0.02780.2347-0.09220.12440.1695-0.02290.0110.0904-0.02280.116735.2479-11.94474.3409
41.60680.4688-0.17480.8244-1.14052.9827-0.04540.2671-0.1691-0.19550.0542-0.1662-0.0460.036-0.03540.2151-0.02760.02550.1632-0.0320.153237.7635-13.0413-5.0287
51.4063-0.00830.13142.5385-0.4941.45270.01240.01750.14890.04960.00250.1743-0.0067-0.10940.01320.1630.01050.02080.15230.00940.144432.53054.0343.171
65.82682.4294-2.6351.7399-1.55064.77580.2094-0.16840.67030.83780.03680.3437-0.598-0.1526-0.1430.30390.05760.06430.2159-0.05330.260731.182112.293513.6992
75.03580.982-0.31871.3828-0.06070.8340.0276-0.42010.24140.3176-0.0605-0.18260.00190.11120.06380.2211-0.0045-0.03360.1834-0.02470.191645.78047.295112.7364
81.77821.73010.41312.04180.2930.26980.1001-0.1506-0.4670.3395-0.1172-0.93760.06550.07830.01280.2833-0.012-0.11070.2892-0.01380.575952.7467-8.60587.3995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 29 )A5 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 74 )A30 - 74
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 103 )A75 - 103
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 127 )A104 - 127
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 188 )A128 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 202 )A189 - 202
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 244 )A203 - 244
8X-RAY DIFFRACTION8chain 'A' and (resid 245 through 266 )A245 - 266

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