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- PDB-5goz: Crystal structure of ZIKV NS5 Methyltransferase in complex with G... -

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Basic information

Entry
Database: PDB / ID: 5goz
TitleCrystal structure of ZIKV NS5 Methyltransferase in complex with GTP and SAH
ComponentsRNA-directed RNA polymerase NS5
KeywordsTRANSFERASE / methyltransferase GTP complex
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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell surface / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / molecular adaptor activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / centrosome / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 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
GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / PYROPHOSPHATE 2- / S-ADENOSYL-L-HOMOCYSTEINE / SUCCINIC ACID / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.049 Å
AuthorsZhang, C. / Jin, T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structure of the NS5 methyltransferase from Zika virus and implications in inhibitor design
Authors: Zhang, C. / Feng, T. / Cheng, J. / Li, Y. / Yin, X. / Zeng, W. / Jin, X. / Li, Y. / Guo, F. / Jin, T.
History
DepositionJul 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase NS5
B: RNA-directed RNA polymerase NS5
C: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,38719
Polymers89,1363
Non-polymers4,25116
Water2,810156
1
A: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8095
Polymers29,7121
Non-polymers1,0984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12380 Å2
MethodPISA
2
B: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0467
Polymers29,7121
Non-polymers1,3346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-10 kcal/mol
Surface area12600 Å2
MethodPISA
3
C: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5327
Polymers29,7121
Non-polymers1,8206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.790, 123.790, 120.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein RNA-directed RNA polymerase NS5 / NS5 Methyltransferase


Mass: 29711.910 Da / Num. of mol.: 3 / Fragment: UNP residues 2524-2785
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, 172 molecules

#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M (NH4)2SO4, 10% PEG 8000, 0.1M SPG buffer

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.049→50 Å / Num. obs: 65414 / % possible obs: 99.8 % / Redundancy: 10 % / Net I/σ(I): 14.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.049→40.52 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.1
RfactorNum. reflection% reflection
Rfree0.2628 1992 3.05 %
Rwork0.2361 --
obs0.2368 65331 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.049→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 264 156 6524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056515
X-RAY DIFFRACTIONf_angle_d1.0448819
X-RAY DIFFRACTIONf_dihedral_angle_d27.1073824
X-RAY DIFFRACTIONf_chiral_restr0.048931
X-RAY DIFFRACTIONf_plane_restr0.0061093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0504-2.10170.33871460.32734530X-RAY DIFFRACTION97
2.1017-2.15850.33141420.32214475X-RAY DIFFRACTION97
2.1585-2.2220.29571440.32574499X-RAY DIFFRACTION97
2.222-2.29370.35721440.36054527X-RAY DIFFRACTION97
2.2937-2.37570.31611450.3084491X-RAY DIFFRACTION97
2.3757-2.47080.25531420.30474506X-RAY DIFFRACTION97
2.4708-2.58320.26721490.30184519X-RAY DIFFRACTION97
2.5832-2.71930.32291370.29684487X-RAY DIFFRACTION97
2.7193-2.88960.32111420.27374528X-RAY DIFFRACTION97
2.8896-3.11260.31561400.26864520X-RAY DIFFRACTION97
3.1126-3.42560.31071390.24444531X-RAY DIFFRACTION97
3.4256-3.92070.24851400.20244534X-RAY DIFFRACTION97
3.9207-4.93730.20531430.17474548X-RAY DIFFRACTION97
4.9373-34.25680.21661390.1994594X-RAY DIFFRACTION97
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)
17.39471.2795-5.75287.75791.09335.05550.00511.65250.3605-0.58570.00120.4278-0.6568-0.9570.02540.45480.0839-0.06170.53290.01850.193715.963869.6421-5.1031
22.3599-0.0757-0.84292.34171.53891.2807-0.23740.22460.158-0.45870.1966-0.1808-0.39820.01320.00480.4416-0.04740.00210.3331-0.02340.246732.694271.55041.1764
30.56340.240.0652.3165-0.15522.0665-0.0339-0.1868-0.07050.13070.0903-0.40030.22010.1716-0.04840.5550.1906-0.1130.5729-0.0110.277134.008959.946918.8331
43.85570.03950.182.44450.73823.1336-0.1192-0.523-0.44150.40770.0945-0.22020.54110.1616-0.01210.61530.1736-0.09040.46540.0680.339933.217950.94120.7777
51.9012-0.2680.35740.63480.45063.43460.0636-0.1264-0.27790.0245-0.0664-0.02980.6994-0.05150.00050.578-0.0002-0.06290.4563-0.00090.27117.788652.308811.5292
61.87460.74130.49971.48310.10850.4991-0.050.00180.05680.00050.0210.1347-0.1216-0.20120.02730.41490.0834-0.0350.453-0.01120.231714.791566.34110.2357
70.2593-0.30090.87087.836-7.19752.0998-0.1758-0.1860.15110.89150.0754-0.0378-0.2788-0.1961-0.01930.66330.2698-0.08650.5848-0.09010.298635.999769.054216.311
83.8591-1.1132-1.48353.63882.45362.70610.25130.68110.0618-0.446-0.3416-0.2138-0.58370.30140.10090.4007-0.0634-0.00340.630.03660.203410.470252.1862-25.1784
94.53542.1696-0.3342.0025-1.2565.98450.0525-0.1786-1.0130.22970.057-0.56931.17980.3682-0.060.53680.1401-0.02460.57220.04730.563415.309532.3132-9.4721
103.32321.6210.01921.47411.13523.1542-0.0257-0.1912-0.63270.2906-0.0713-0.12791.0109-0.32040.05031.0441-0.1421-0.02680.60740.11790.32993.102138.27671.872
112.3340.73992.39590.34570.59726.68730.0896-0.2905-0.8430.24210.1072-0.18071.3225-0.3386-0.18881.2043-0.04550.08690.55480.12770.5583-1.200628.7556-3.3891
121.58310.3570.1682.3932-1.1394.3391-0.044-0.0524-0.20880.21930.0640.15360.3775-0.5061-0.03910.445-0.1245-0.01460.57210.02620.2761-7.493245.32-8.1324
132.2956-0.62560.05081.22130.34321.6897-0.0284-0.09150.09810.1961-0.0613-0.08620.0575-0.10930.08920.4155-0.0484-0.02960.42670.03570.2083.043256.0014-9.5327
142.91791.5474-1.25752.6657-1.90624.29140.1933-0.0272-0.19770.6337-0.3782-0.37110.36820.43780.16190.77130.0972-0.20150.4653-0.05760.522416.90839.8997-5.4074
152.9275-0.1958-0.62460.7927-1.15093.98260.1097-0.63510.11360.25760.0121-0.0001-0.55290.3221-0.10740.50620.143-0.08010.585-0.14830.29550.225786.659310.9368
164.14671.2706-1.27960.89131.48237.3321-0.1430.2506-1.2247-0.26790.119-0.26211.08130.19810.03240.76980.1887-0.04840.5064-0.0880.640347.864463.9828-7.9623
171.4441-0.6850.14871.2174-0.2840.1137-0.14760.1764-0.3688-0.22350.05710.06450.48540.41160.04571.26630.5224-0.09721.1364-0.224-0.027559.150875.9449-15.5613
182.70310.15211.94671.69790.16962.255-0.01-0.1372-0.3006-0.44110.0903-0.14010.47970.6697-0.08661.05320.40430.00290.7859-0.16170.585762.932864.3147-10.766
190.2080.02060.44821.04270.20661.0310.03310.1597-0.1375-0.386-0.0008-0.41480.43020.8235-0.08240.84980.33530.02880.9556-0.08360.421669.760176.9089-5.6463
202.65620.59040.59261.17810.1550.996-0.13370.11550.1069-0.18540.0563-0.0672-0.21040.38950.05710.56880.1056-0.05640.6129-0.09830.340164.385488.199-4.5558
214.23924.0909-0.3866.0309-3.254.01460.1569-0.44510.68920.12430.02940.5322-0.6305-0.0418-0.17170.53480.179-0.15430.4949-0.21160.463350.610193.92652.0809
222.73160.5784-1.2091.60761.51746.198-0.32320.132-0.1676-0.2050.1281-0.11230.23550.1550.12380.47330.048-0.08730.4001-0.03570.428744.596374.7639-9.0519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 127 )
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 188 )
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 245 )
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 265 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 28 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 46 )
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 103 )
11X-RAY DIFFRACTION11chain 'B' and (resid 104 through 123 )
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 188 )
13X-RAY DIFFRACTION13chain 'B' and (resid 189 through 244 )
14X-RAY DIFFRACTION14chain 'B' and (resid 245 through 264 )
15X-RAY DIFFRACTION15chain 'C' and (resid 4 through 32 )
16X-RAY DIFFRACTION16chain 'C' and (resid 33 through 56 )
17X-RAY DIFFRACTION17chain 'C' and (resid 57 through 103 )
18X-RAY DIFFRACTION18chain 'C' and (resid 104 through 127 )
19X-RAY DIFFRACTION19chain 'C' and (resid 128 through 153 )
20X-RAY DIFFRACTION20chain 'C' and (resid 154 through 228 )
21X-RAY DIFFRACTION21chain 'C' and (resid 229 through 245 )
22X-RAY DIFFRACTION22chain 'C' and (resid 246 through 264 )

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