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- PDB-8y9v: ZIKV NS2B/NS3 protease -

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Basic information

Entry
Database: PDB / ID: 8y9v
TitleZIKV NS2B/NS3 protease
Components
  • (Serine protease NS3) x 2
  • DAR-LYS-ORN-ARG
  • Serine protease subunit NS2B
KeywordsHYDROLASE / ZIKV / NS2B/NS3 protease
Function / homology
Function and homology information


symbiont-mediated suppression of host interferon-mediated signaling pathway / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity ...symbiont-mediated suppression of host interferon-mediated signaling pathway / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / protein-macromolecule adaptor activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / viral envelope / lipid binding / symbiont entry into host cell / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 / 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
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, C.Y. / Xu, Q. / Wang, W.W. / Zhou, H. / Wang, Q.S.
Funding support China, 1items
OrganizationGrant numberCountry
Other government21ZR1471800 China
CitationJournal: To Be Published
Title: Crystallographic data collection using a multilayer monochromator on an undulator beamline at SSRF
Authors: Zhang, C.Y. / Xu, Q. / Liang, M. / Yu, L. / Li, M.J. / Zhu, Z.M. / Huang, L.Q. / Li, Q.H. / Yu, F. / Wang, Y.Z. / Zhou, H. / Wang, Q.S.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease subunit NS2B
B: Serine protease NS3
C: Serine protease subunit NS2B
D: Serine protease NS3
E: DAR-LYS-ORN-ARG


Theoretical massNumber of molelcules
Total (without water)45,9475
Polymers45,9475
Non-polymers00
Water2,936163
1
A: Serine protease subunit NS2B
B: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)22,2202
Polymers22,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-28 kcal/mol
Surface area9190 Å2
MethodPISA
2
C: Serine protease subunit NS2B
D: Serine protease NS3
E: DAR-LYS-ORN-ARG


Theoretical massNumber of molelcules
Total (without water)23,7273
Polymers23,7273
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-24 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.753, 59.753, 213.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serine protease subunit NS2B


Mass: 5865.384 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8XX12
#2: Protein Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 16354.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Protein Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 17285.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#4: Protein/peptide DAR-LYS-ORN-ARG


Mass: 575.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: PEG 20% 2000, ammonium sulfate 0.2 M, sodium acetate trihydrate 0.1 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.924 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.924 Å / Relative weight: 1
ReflectionResolution: 1.9→45.77 Å / Num. obs: 31750 / % possible obs: 99.7 % / Redundancy: 24.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.527 / Rpim(I) all: 0.108 / Rrim(I) all: 0.539 / Χ2: 1.04 / Net I/σ(I): 7.3 / Num. measured all: 787827
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 94.9 % / Redundancy: 22 % / Rmerge(I) obs: 6.765 / Num. measured all: 42472 / Num. unique obs: 1929 / CC1/2: 0.057 / Rpim(I) all: 1.456 / Rrim(I) all: 6.933 / Χ2: 1.06 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.77 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1992 6.31 %
Rwork0.217 --
obs0.219 31573 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 0 163 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082956
X-RAY DIFFRACTIONf_angle_d1.0624003
X-RAY DIFFRACTIONf_dihedral_angle_d8.084417
X-RAY DIFFRACTIONf_chiral_restr0.069445
X-RAY DIFFRACTIONf_plane_restr0.01516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.36731290.36331957X-RAY DIFFRACTION93
1.95-20.36151400.31772085X-RAY DIFFRACTION100
2-2.060.31081400.2922074X-RAY DIFFRACTION100
2.06-2.120.33731400.29432070X-RAY DIFFRACTION100
2.12-2.20.29061400.25812074X-RAY DIFFRACTION100
2.2-2.290.31031400.27512078X-RAY DIFFRACTION100
2.29-2.390.27711430.23282112X-RAY DIFFRACTION100
2.39-2.520.29391410.23882085X-RAY DIFFRACTION100
2.52-2.680.25221420.242107X-RAY DIFFRACTION100
2.68-2.880.251430.22292118X-RAY DIFFRACTION100
2.88-3.170.26731440.20292136X-RAY DIFFRACTION100
3.17-3.630.23131450.18852139X-RAY DIFFRACTION100
3.63-4.570.1891480.16052193X-RAY DIFFRACTION100
4.57-45.770.20361570.1932353X-RAY DIFFRACTION100
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)
18.9027-1.9372.3156.41981.28493.5618-0.25620.4613-0.6344-0.34210.00721.66921.0052-0.5713-0.25930.8209-0.0922-0.14060.30140.0110.49067.2135-31.6954-12.6963
22.58641.8288-0.11122.75552.13853.12860.12260.9178-0.2706-0.97230.34940.0438-0.0869-0.1539-0.12250.39450.075-0.01170.3248-0.05980.323818.9001-21.8428-28.289
34.3226-3.2256-2.03567.78696.16039.444-0.08980.88250.3232-0.73480.2409-0.06180.1970.5128-0.3420.4503-0.0128-0.05330.44190.00920.376210.0584-4.4596-28.0524
41.58350.30980.46343.3852-0.73232.7545-0.417-1.01180.38640.73280.3288-0.2084-0.5505-0.0215-0.2580.44950.1591-0.01820.4407-0.01830.29544.6322-3.045-8.5434
52.0603-1.75321.33431.6182-1.03271.85940.16730.6297-1.0806-0.3145-0.1136-0.02440.05050.17130.04880.4702-0.095-0.12970.2496-0.03470.429816.089-31.2813-16.6819
61.81580.07230.81682.3184-0.16084.11150.1281-0.1829-0.20180.08610.0403-0.01010.6341-0.034-0.12390.26570.0187-0.03740.24910.02720.208912.9563-22.4857-8.238
71.7534-1.08110.50543.4195-1.33672.3807-0.03090.20930.0874-0.2148-0.0590.0342-0.06290.15140.07750.21540.00210.00330.2031-0.00280.202915.5542-12.8563-21.6128
83.3037-1.20650.04641.44080.01972.8591-0.0233-0.0050.2813-0.1682-0.0025-0.2166-0.03810.00660.03080.195-0.031-0.02970.17650.01550.206510.0924-10.0363-19.622
91.5706-0.77680.5932.8704-0.19351.0529-0.6484-1.61710.16450.88370.1143-0.9735-0.23151.02130.35630.32360.0428-0.13970.76260.05410.357622.7801-13.373-8.7484
107.24152.51155.29693.45161.2494.00480.0843-0.3886-0.5773-0.24610.01270.17050.1808-0.2434-0.04271.54640.10820.39880.62530.02231.61931.4201-12.3853-14.5583
112.7212-0.32440.15256.75190.89915.76640.1908-0.0322-0.08530.0323-0.02870.32340.2401-0.8301-0.04030.1722-0.00270.03090.31690.06890.30894.8726-19.802419.0115
124.479-3.80371.17583.6801-0.56660.8288-0.9041-2.3129-0.78141.53821.14520.83380.5202-1.2898-0.07090.62510.11310.02840.6899-0.03590.393321.0603-13.484831.9481
132.2175-0.75850.61832.21060.68483.65980.34070.3313-0.3474-0.28080.0258-0.4320.37170.5237-0.27710.32510.0859-0.02970.35750.0030.297133.6245-23.821711.6651
142.1803-0.6285-0.12091.7885-1.71463.8689-0.02550.2676-0.2666-0.20230.06270.30490.0842-0.4863-0.02490.1840.0077-0.02960.28460.0040.23097.7541-19.915512.2643
151.7088-0.08940.62630.18230.00051.7287-0.1341-0.05650.12890.041-0.0004-0.1213-0.3994-0.05470.12140.27360.0506-0.01370.19780.03190.255120.0004-12.52212.0563
162.740.48961.00442.6517-0.34262.06720.1357-0.11910.09740.1873-0.1115-0.0188-0.23520.07910.03090.1940.0169-0.00040.20690.02180.189122.8606-18.110621.1289
175.23020.06420.18262.01891.82613.97980.3289-0.0937-0.5685-0.1437-0.25030.20910.3720.3435-0.05780.2128-0.0092-0.0080.27570.05250.251226.2342-20.720715.8195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 7 through 11 )
2X-RAY DIFFRACTION2chain 'C' and (resid 12 through 21 )
3X-RAY DIFFRACTION3chain 'C' and (resid 22 through 31 )
4X-RAY DIFFRACTION4chain 'C' and (resid 32 through 44 )
5X-RAY DIFFRACTION5chain 'D' and (resid 13 through 34 )
6X-RAY DIFFRACTION6chain 'D' and (resid 35 through 79 )
7X-RAY DIFFRACTION7chain 'D' and (resid 80 through 118 )
8X-RAY DIFFRACTION8chain 'D' and (resid 119 through 163 )
9X-RAY DIFFRACTION9chain 'D' and (resid 164 through 173 )
10X-RAY DIFFRACTION10chain 'E' and (resid 2 through 4 )
11X-RAY DIFFRACTION11chain 'A' and (resid 7 through 16 )
12X-RAY DIFFRACTION12chain 'A' and (resid 17 through 26 )
13X-RAY DIFFRACTION13chain 'A' and (resid 27 through 45 )
14X-RAY DIFFRACTION14chain 'B' and (resid 18 through 71 )
15X-RAY DIFFRACTION15chain 'B' and (resid 72 through 94 )
16X-RAY DIFFRACTION16chain 'B' and (resid 95 through 155 )
17X-RAY DIFFRACTION17chain 'B' and (resid 156 through 170 )

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