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- PDB-7iar: Crystal structure of Zika NS2B-NS3 protease in complex with fragm... -

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Basic information

Entry
Database: PDB / ID: 7iar
TitleCrystal structure of Zika NS2B-NS3 protease in complex with fragment EOS102546 from ECBL-96
Components
  • NS2B co-factor
  • NS3 protease
KeywordsVIRAL PROTEIN / crystallographic fragment screening / NS2B-NS3 Zika protease / ECBL-96 fragment library
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / symbiont entry into host cell / GTP binding / 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 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
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBenz, L.S. / Wollenhaupt, J. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FE2166/1-1 Germany
CitationJournal: Rsc Med Chem / Year: 2025
Title: From fragments to follow-ups: rapid hit expansion by making use of EU-OPENSCREEN resources.
Authors: Benz, L.S. / Wollenhaupt, J. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.
History
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS2B co-factor
B: NS3 protease
C: NS2B co-factor
D: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7686
Polymers49,4864
Non-polymers2822
Water2,288127
1
A: NS2B co-factor
B: NS3 protease


Theoretical massNumber of molelcules
Total (without water)24,7432
Polymers24,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-29 kcal/mol
Surface area9280 Å2
MethodPISA
2
C: NS2B co-factor
D: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0254
Polymers24,7432
Non-polymers2822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-27 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.170, 60.170, 214.800
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 NS2B co-factor


Mass: 5865.384 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A142IX72
#2: Protein NS3 protease


Mass: 18877.396 Da / Num. of mol.: 2 / Mutation: C143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A142IX72
#3: Chemical ChemComp-A1CD1 / 2-(5-methylthiophen-2-yl)ethan-1-amine


Mass: 141.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 0.2 M ammonium sulfate, 24 % (w/v) PEG 2000
Time: 2-3 days

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→46.06 Å / Num. obs: 43351 / % possible obs: 97 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.116 / Net I/σ(I): 13.66 / Num. measured all: 388089
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
1.7-1.892.31.0975360165180.5811.1631.56
1.8-1.9395.30.7035036163470.7420.7482.55
1.93-2.08970.4275393260480.9040.4524.74
2.08-2.2899.10.2795517756890.9640.2958.19
2.28-2.5599.20.2045081251870.9790.21511.37
2.55-2.9499.40.1314059146350.9930.13916.96
2.94-3.698.90.0713897239590.9980.07531.36
3.6-5.0798.20.0432754831090.9990.04545.4
5.0797.50.0331709518590.9990.03547.22

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.06 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 2099 4.84 %
Rwork0.1944 --
obs0.196 43342 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 18 127 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043005
X-RAY DIFFRACTIONf_angle_d0.7074072
X-RAY DIFFRACTIONf_dihedral_angle_d6.115431
X-RAY DIFFRACTIONf_chiral_restr0.051448
X-RAY DIFFRACTIONf_plane_restr0.006531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.30021270.30962499X-RAY DIFFRACTION90
1.74-1.780.29781300.27912566X-RAY DIFFRACTION93
1.78-1.830.25641350.26612633X-RAY DIFFRACTION95
1.83-1.880.29231350.24422653X-RAY DIFFRACTION95
1.88-1.950.27251350.23512663X-RAY DIFFRACTION95
1.95-2.020.22651380.21532701X-RAY DIFFRACTION97
2.02-2.10.25411390.22462744X-RAY DIFFRACTION98
2.1-2.190.25951420.20182785X-RAY DIFFRACTION99
2.19-2.310.22741420.19592789X-RAY DIFFRACTION99
2.31-2.450.27791410.19822778X-RAY DIFFRACTION99
2.45-2.640.23611450.20842833X-RAY DIFFRACTION99
2.64-2.910.24261420.2062820X-RAY DIFFRACTION99
2.91-3.330.23641460.18832857X-RAY DIFFRACTION99
3.33-4.190.1691460.16132869X-RAY DIFFRACTION98
4.19-46.060.19771560.16043053X-RAY DIFFRACTION98
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)
14.55271.30380.49153.52162.16365.72650.1668-0.4651-0.0460.2825-0.2794-0.3295-0.26970.9395-0.06280.2408-0.1036-0.04120.31540.10890.276328.3867-35.522440.8582
23.30060.5770.06470.10870.16122.8869-0.0638-0.0056-0.0627-0.23970.22910.8719-0.2204-0.40630.05810.13550.0601-0.00440.33380.07410.3798-2.5924-42.433737.8642
33.28371.0367-0.72476.3771-0.54455.04070.04420.0222-0.1417-0.00610.01220.04030.0107-0.1779-0.0080.1047-0.00940.00720.17730.01710.12797.2832-43.118141.3877
45.54661.3492-0.03864.45020.1592.90320.1624-0.02650.11180.19-0.07590.3922-0.1075-0.5866-0.04360.15510.00080.04510.26090.04030.13615.4456-42.954448.1329
54.4702-0.5443-0.99430.96980.12122.6562-0.1030.1947-0.065-0.0588-0.0826-0.10950.24530.24420.21760.1425-0.0515-0.0060.1655-0.0160.206514.0171-47.053433.0266
65.83992.72921.24154.20061.49426.7514-0.08920.3483-0.3156-0.18120.1531-0.1790.00880.3650.01180.15470.03490.02330.18490.06560.159623.0739-42.879930.0633
71.3898-0.3625-0.79472.91830.02311.5349-0.1173-0.1361-0.05850.1933-0.0123-0.2640.10920.2520.16240.15340.01850.00420.19860.0560.166520.2599-38.923235.4609
83.56512.1416-0.81055.557-0.78752.72480.07180.0396-0.1960.1203-0.1773-0.04260.04840.1540.0820.11090.0178-0.00990.17440.03050.141918.982-42.862835.1245
95.0469-0.1241-0.78832.73530.16190.2473-0.0929-0.65760.27420.23260.06260.2555-0.0839-0.1292-0.0150.16930.00090.06040.26930.050.166312.4208-16.409225.6781
104.6079-1.84690.81642.3810.66665.59290.37410.4256-0.2265-0.11680.0809-0.27830.3870.6096-0.4490.18960.0522-0.02680.20680.0040.230833.5677-23.804413.1667
112.88820.0344-0.3877.3477-0.21634.1195-0.02640.0059-0.25540.07220.06280.40160.1792-0.34070.00020.0959-0.0104-0.00670.19310.0270.15436.3211-21.878317.8726
123.5947-1.6526-0.40828.66351.2764.44130.04020.0651-0.1563-0.3520.0660.2257-0.0826-0.1803-0.09730.12330.0126-0.01180.15590.01280.128512.3112-18.626510.6347
138.7616-0.1005-1.35673.4452-0.96822.54150.173-0.03210.0071-0.05130.06190.36750.1161-0.7826-0.20160.1844-0.0187-0.06810.39470.02170.18175.1121-19.5356.8224
143.6427-0.27822.33920.88780.16374.0997-0.08860.18520.317-0.10420.0047-0.0387-0.34220.06050.12460.15370.01020.02280.12270.0470.174219.4995-12.883111.2336
157.36626.7134-0.06197.96880.48453.0320.2042-0.6574-0.13040.3357-0.1983-0.06050.0260.041-0.07590.1590.0558-0.01460.25530.04520.150616.0058-19.492327.388
166.9443-0.7457-2.48143.76071.26272.40.2488-0.27410.36260.07790.0189-0.2196-0.3899-0.0545-0.17310.1025-0.0012-0.04680.16730.04370.085928.3188-17.090822.757
174.24121.3230.91683.2686-0.24181.65420.01390.2421-0.0815-0.0695-0.0647-0.1444-0.0405-0.00720.12490.1516-0.0087-0.01730.16250.03020.157625.173-21.434217.9376
183.30273.45564.0774.4124.71035.42410.1606-0.42160.59910.1881-0.1972-0.2553-0.76420.18610.17680.2597-0.03560.04330.24270.00110.255520.2816-8.527622.6156
196.0556-0.8194-0.24914.21571.80343.6760.0884-0.0051-0.15140.01020.086-0.15260.12390.2115-0.05160.1230.0029-0.02410.16490.01660.11824.3926-19.73215.7419
205.8791-0.27950.46052.7497-0.69842.7278-0.17550.7057-0.1167-0.17910.07240.1410.1876-0.1509-0.03750.1531-0.0334-0.0440.30130.03840.20357.4294-44.390728.5071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 70 through 88 )
2X-RAY DIFFRACTION2chain 'D' and (resid 13 through 34 )
3X-RAY DIFFRACTION3chain 'D' and (resid 35 through 53 )
4X-RAY DIFFRACTION4chain 'D' and (resid 54 through 79 )
5X-RAY DIFFRACTION5chain 'D' and (resid 80 through 106 )
6X-RAY DIFFRACTION6chain 'D' and (resid 107 through 118 )
7X-RAY DIFFRACTION7chain 'D' and (resid 119 through 137 )
8X-RAY DIFFRACTION8chain 'D' and (resid 138 through 170 )
9X-RAY DIFFRACTION9chain 'A' and (resid 50 through 69 )
10X-RAY DIFFRACTION10chain 'A' and (resid 70 through 88 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 42 )
12X-RAY DIFFRACTION12chain 'B' and (resid 43 through 53 )
13X-RAY DIFFRACTION13chain 'B' and (resid 54 through 71 )
14X-RAY DIFFRACTION14chain 'B' and (resid 72 through 93 )
15X-RAY DIFFRACTION15chain 'B' and (resid 94 through 106 )
16X-RAY DIFFRACTION16chain 'B' and (resid 107 through 118 )
17X-RAY DIFFRACTION17chain 'B' and (resid 119 through 137 )
18X-RAY DIFFRACTION18chain 'B' and (resid 138 through 145 )
19X-RAY DIFFRACTION19chain 'B' and (resid 146 through 170 )
20X-RAY DIFFRACTION20chain 'C' and (resid 50 through 69 )

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