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- PDB-5gp1: Crystal structure of ZIKV NS5 Methyltransferase in complex with G... -

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Basic information

Entry
Database: PDB / ID: 5gp1
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 / double-stranded RNA binding / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / host cell surface / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / molecular adaptor activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / 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 / 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 NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / 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 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
Chem-GTA / NICKEL (II) ION / S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.444 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)93,47818
Polymers89,1363
Non-polymers4,34315
Water1,26170
1
A: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3648
Polymers29,7121
Non-polymers1,6527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-38 kcal/mol
Surface area12670 Å2
MethodPISA
2
B: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0765
Polymers29,7121
Non-polymers1,3644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-31 kcal/mol
Surface area12200 Å2
MethodPISA
3
C: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0395
Polymers29,7121
Non-polymers1,3274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.770, 123.770, 119.360
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 / Production host: Escherichia coli (E. coli) / References: UniProt: H9A910, UniProt: A0A024B7W1*PLUS

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Non-polymers , 5 types, 85 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GTA / P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / 7-METHYL-GPPPA


Mass: 787.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N10O17P3
#4: 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
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
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 PILATUS 6M-F / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 38127 / % possible obs: 99.1 % / Redundancy: 8.2 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.444→48.892 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.78 / Stereochemistry target values: TWIN_LSQ_F
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2803 3957 5.3 %
Rwork0.2369 --
obs0.2389 37348 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.444→48.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6098 0 272 70 6440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036504
X-RAY DIFFRACTIONf_angle_d0.68810
X-RAY DIFFRACTIONf_dihedral_angle_d22.1843799
X-RAY DIFFRACTIONf_chiral_restr0.039936
X-RAY DIFFRACTIONf_plane_restr0.0031083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4462-2.48840.3721680.31913021X-RAY DIFFRACTION79
2.4884-2.53360.44281880.3313561X-RAY DIFFRACTION95
2.5336-2.58230.45941980.33693608X-RAY DIFFRACTION95
2.5823-2.6350.3782000.33363497X-RAY DIFFRACTION94
2.635-2.69230.37491980.31543569X-RAY DIFFRACTION94
2.6923-2.75490.28822020.29243545X-RAY DIFFRACTION94
2.7549-2.82380.33041920.30333582X-RAY DIFFRACTION94
2.8238-2.90010.34621900.2793520X-RAY DIFFRACTION95
2.9001-2.98540.30591970.26093595X-RAY DIFFRACTION94
2.9854-3.08170.30251970.27163572X-RAY DIFFRACTION94
3.0817-3.19180.34321980.2533578X-RAY DIFFRACTION95
3.1918-3.31950.33891990.2483563X-RAY DIFFRACTION95
3.3195-3.47040.2531920.23493548X-RAY DIFFRACTION95
3.4704-3.65320.27312040.22643588X-RAY DIFFRACTION94
3.6532-3.88190.23331980.21563559X-RAY DIFFRACTION95
3.8819-4.18120.22012120.20133544X-RAY DIFFRACTION94
4.1812-4.60110.25641950.1853595X-RAY DIFFRACTION95
4.6011-5.26510.26412060.18493555X-RAY DIFFRACTION94
5.2651-6.62660.23921980.22653572X-RAY DIFFRACTION95
6.6266-35.73310.20542030.21213563X-RAY DIFFRACTION94
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)
10.2041-0.1196-0.42040.3940.77641.73280.0254-0.1328-0.04160.07820.06930.01030.18670.2961-0.06260.5358-0.1791-0.09850.60940.12780.230349.9847126.11048.0064
27.3629-7.25043.08578.6957-2.9332.43630.60050.0818-0.0738-0.7714-0.30540.57080.1387-1.5461-0.28530.5330.09020.0011.021-0.03040.262436.1027140.6828-7.9962
30.70940.31770.67330.72610.83091.21620.048-0.02720.0103-0.2355-0.15770.1395-0.0137-0.47940.05780.5736-0.0314-0.05970.71460.07530.178936.3548128.2223-17.5535
40.16860.36210.1690.99750.20773.37640.08180.06750.0751-0.4056-0.15380.32070.1371-0.77320.04320.4919-0.0018-0.10541.06710.0620.331427.5659126.6279-18.2312
50.377-0.4242-0.21910.51750.04381.87260.04910.0987-0.1365-0.2072-0.20420.28860.3468-1.0770.140.6744-0.1787-0.05390.92410.00040.266431.5238115.5983-10.0078
60.29450.0588-0.01021.0723-0.09970.86240.01460.09870.0252-0.1744-0.0750.03950.0915-0.13160.06140.462-0.0239-0.03350.60210.08680.132545.2997119.8068-8.7172
70.01670.0328-0.09290.28150.02980.70970.00320.007-0.0207-0.0152-0.02690.04520.0646-0.1525-0.07530.4057-0.01990.05260.52130.08970.105138.7421156.57319.3792
80.75120.5278-0.91131.6353-0.13631.5356-0.03680.23810.0094-0.28350.05310.0873-0.072-0.5193-0.02040.31910.07080.05790.78510.03870.218326.0629164.441513.5129
90.132-0.01530.02130.13830.15010.1728-0.0060.01870.00670.0426-0.03510.0026-0.0774-0.0405-0.03890.4267-0.00260.02950.45260.06850.080445.427169.7666.2244
103.1804-1.3278-0.76770.99110.78410.8875-0.0251-0.36560.1083-0.05180.1203-0.02210.05150.2707-0.11060.492-0.07560.04320.50970.03580.147342.0029148.44512.5593
110.16390.0372-0.41540.0093-0.11061.2013-0.065-0.0306-0.09530.0189-0.0299-0.00370.33890.1111-0.07610.5352-0.0674-0.04720.47430.10570.147469.3347147.811228.9379
120.32360.1292-0.21810.9675-1.7143.03570.0233-0.0521-0.187-0.0918-0.02020.05760.5963-0.3959-0.03560.5756-0.1522-0.04510.49490.03750.177455.9064145.738328.9325
130.1295-0.0361-0.16160.02740.06580.3277-0.063-0.06690.00060.07820.0289-0.0077-0.00960.0013-0.03020.4441-0.018-0.04330.43760.06810.097862.6101161.805628.2773
143.82230.9715-0.07492.5258-1.12630.69630.1946-0.0744-0.04650.0675-0.5335-0.22020.34550.63730.35860.86330.0149-0.15770.37980.02670.258578.9085148.751629.22
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 127 )
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 153 )
6X-RAY DIFFRACTION6chain 'A' and (resid 154 through 265 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 103 )
8X-RAY DIFFRACTION8chain 'B' and (resid 104 through 145 )
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 245 )
10X-RAY DIFFRACTION10chain 'B' and (resid 246 through 265 )
11X-RAY DIFFRACTION11chain 'C' and (resid 4 through 103 )
12X-RAY DIFFRACTION12chain 'C' and (resid 104 through 171 )
13X-RAY DIFFRACTION13chain 'C' and (resid 172 through 242 )
14X-RAY DIFFRACTION14chain 'C' and (resid 243 through 264 )

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