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- PDB-5wz1: Crystal structure of Zika virus NS5 methyltransferase bound to S-... -

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Basic information

Entry
Database: PDB / ID: 5wz1
TitleCrystal structure of Zika virus NS5 methyltransferase bound to S-adenosyl-L-methionine
ComponentsNS5 methyltransferase
KeywordsTRANSFERASE / zika virus / methyltransferase / MTase / SAM
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / 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 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: 2.507 Å
AuthorsDuan, W. / Song, H. / Qi, J. / Shi, Y. / Gao, G.F.
CitationJournal: EMBO J. / Year: 2017
Title: The crystal structure of Zika virus NS5 reveals conserved drug targets.
Authors: Duan, W. / Song, H. / Wang, H. / Chai, Y. / Su, C. / Qi, J. / Shi, Y. / Gao, G.F.
History
DepositionJan 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name / _diffrn_detector.detector
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: NS5 methyltransferase
D: NS5 methyltransferase
E: NS5 methyltransferase
F: NS5 methyltransferase
G: NS5 methyltransferase
H: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,71616
Polymers245,5288
Non-polymers3,1878
Water00
1
A: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0892
Polymers30,6911
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0892
Polymers30,6911
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0892
Polymers30,6911
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0892
Polymers30,6911
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0892
Polymers30,6911
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0892
Polymers30,6911
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0892
Polymers30,6911
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: NS5 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0892
Polymers30,6911
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.549, 86.847, 107.556
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NS5 methyltransferase / Genome polyprotein


Mass: 30691.004 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 2525-2794
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A140E7U5, UniProt: A0A109PRQ3*PLUS
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C15H22N6O5S

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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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 66444 / % possible obs: 98.6 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.195 / Net I/σ(I): 8.075

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9K

1l9k


Resolution: 2.507→45.447 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 50.32
RfactorNum. reflection% reflection
Rfree0.2568 3372 5.33 %
Rwork0.2351 --
obs0.2468 63210 93.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.507→45.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16168 0 216 0 16384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416720
X-RAY DIFFRACTIONf_angle_d0.71922560
X-RAY DIFFRACTIONf_dihedral_angle_d12.7616344
X-RAY DIFFRACTIONf_chiral_restr0.0292424
X-RAY DIFFRACTIONf_plane_restr0.0042856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5107-2.5540.3154960.3142034X-RAY DIFFRACTION60
2.554-2.60040.30831380.30832317X-RAY DIFFRACTION70
2.6004-2.65040.3241370.30612574X-RAY DIFFRACTION77
2.6504-2.70450.37021580.31752769X-RAY DIFFRACTION82
2.7045-2.76330.30341620.2943030X-RAY DIFFRACTION90
2.7633-2.82760.34281650.28693065X-RAY DIFFRACTION92
2.8276-2.89830.28361730.27993079X-RAY DIFFRACTION93
2.8983-2.97660.29921580.27463111X-RAY DIFFRACTION93
2.9766-3.06420.30611800.27213137X-RAY DIFFRACTION93
3.0642-3.16310.29981580.26413178X-RAY DIFFRACTION94
3.1631-3.27610.28391460.26333134X-RAY DIFFRACTION94
3.2761-3.40720.25781800.25653119X-RAY DIFFRACTION93
3.4072-3.56220.2741690.23873155X-RAY DIFFRACTION93
3.5622-3.74990.2541840.23863134X-RAY DIFFRACTION93
3.7499-3.98470.23741390.22993171X-RAY DIFFRACTION94
3.9847-4.29210.2511930.20993118X-RAY DIFFRACTION93
4.2921-4.72360.2061780.2013163X-RAY DIFFRACTION94
4.7236-5.4060.23541670.21293211X-RAY DIFFRACTION94
5.406-6.80680.25931620.23423211X-RAY DIFFRACTION94
6.8068-43.57080.25751600.24033237X-RAY DIFFRACTION93
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)
10.30990.04510.10150.29910.09640.303-0.10470.04290.0329-0.0096-0.05750.10080.1050.0647-0.48960.05010.02060.0570.06880.01190.0472-3.797-1.7827-1.3709
20.13540.0957-0.09530.727-0.4430.3937-0.0032-0.05880.01020.05050.0780.20410.0719-0.01370.33150.10160.0166-0.03340.1276-0.06290.0877-10.7667-1.806851.9932
30.01630.00110.01140.24080.01250.1556-0.0406-0.06940.0833-0.1652-0.04380.173-0.02920.0124-0.02980.0980.0042-0.04090.1491-0.01520.1209-29.583417.727122.3413
40.12320.02020.10260.2146-0.05530.1344-0.03150.03080.10350.0309-0.1040.01850.0619-0.0212-0.00030.1718-0.01210.04520.1631-0.00290.1842-29.9897-25.166731.7226
50.1870.05140.0710.27080.07190.09220.03750.09270.05160.21270.019-0.1811-0.150.02620.0350.209-0.0101-0.00470.11730.02810.107322.6375-25.711130.9272
60.1178-0.07450.10210.2693-0.05770.19480.0104-0.03950.0833-0.0814-0.1368-0.09990.1680.0005-0.02760.1802-0.00660.03270.14090.00020.135723.146818.276721.6418
70.10320.08770.03050.13870.04080.1159-0.1144-0.02180.0728-0.1371-0.0046-0.07430.01790.0206-0.06590.0749-0.08750.01380.2725-0.06030.2728-59.0201-3.52770.4715
80.2576-0.02380.11320.4104-0.01380.11050.0589-0.0378-0.0372-0.3718-0.0021-0.03860.0751-0.02370.02560.1525-0.043-0.00470.1422-0.05230.297541.9548-3.551554.0791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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