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- PDB-7ib1: Crystal structure of Zika NS2B-NS3 protease in complex with fragm... -

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Basic information

Entry
Database: PDB / ID: 7ib1
TitleCrystal structure of Zika NS2B-NS3 protease in complex with fragment EOS102869 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: 1.65 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)49,6565
Polymers49,4864
Non-polymers1701
Water2,486138
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 area3910 Å2
ΔGint-26 kcal/mol
Surface area8940 Å2
MethodPISA
2
C: NS2B co-factor
D: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9133
Polymers24,7432
Non-polymers1701
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-25 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.620, 60.620, 214.920
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-A1CDT / N-(2-aminoethyl)thiophene-2-carboxamide


Mass: 170.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N2OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2 Å3/Da / Density % sol: 38.5 %
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: 1.65→40.21 Å / Num. obs: 49433 / % possible obs: 100 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.106 / Net I/σ(I): 15.09 / Num. measured all: 549640
Reflection shell

Diffraction-ID: 1 / % possible obs: 100 %

Resolution (Å)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
1.65-1.751.0779014678320.6981.1271.86
1.75-1.870.6378406973640.8650.6673.21
1.87-2.020.3787463769070.9510.3975.5
2.02-2.210.2397631963530.9820.2499.74
2.21-2.470.1646735158010.9920.17214.44
2.47-2.850.1165293951630.9950.12219.62
2.85-3.490.0684846644100.9990.07134.83
3.49-4.930.0463490535040.9990.04847.43

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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: 1.65→40.21 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 2099 4.25 %
Rwork0.187 --
obs0.1879 49424 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 11 138 3042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012979
X-RAY DIFFRACTIONf_angle_d1.084037
X-RAY DIFFRACTIONf_dihedral_angle_d6.716424
X-RAY DIFFRACTIONf_chiral_restr0.068445
X-RAY DIFFRACTIONf_plane_restr0.009526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.37611370.31633086X-RAY DIFFRACTION100
1.69-1.730.27941370.27893101X-RAY DIFFRACTION100
1.73-1.780.27481370.2353088X-RAY DIFFRACTION100
1.78-1.830.2251380.21583098X-RAY DIFFRACTION100
1.83-1.890.26561370.20323093X-RAY DIFFRACTION100
1.89-1.960.22521390.20033129X-RAY DIFFRACTION100
1.96-2.030.22671370.19743100X-RAY DIFFRACTION100
2.03-2.130.25581370.21023095X-RAY DIFFRACTION100
2.13-2.240.20621400.1753155X-RAY DIFFRACTION100
2.24-2.380.17751400.1763146X-RAY DIFFRACTION100
2.38-2.560.2121390.19023143X-RAY DIFFRACTION100
2.56-2.820.22831410.19333175X-RAY DIFFRACTION100
2.82-3.230.2021430.19123206X-RAY DIFFRACTION100
3.23-4.070.1861440.16363261X-RAY DIFFRACTION100
4.07-40.210.16971530.16643449X-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)
13.4141-0.6703-1.21522.82150.26340.44210.3129-0.44320.4030.4736-0.2952-0.4049-0.59831.029-0.03810.3062-0.1856-0.0220.50480.0370.247327.9737-34.739944.1218
21.13570.89460.07131.34790.01530.3105-0.06130.3176-0.26650.20810.3250.73040.1313-0.2239-0.30850.2291-0.0234-0.0030.25150.04750.3774-1.1675-49.895236.6954
32.85431.17380.39152.80450.30963.46220.1488-0.03930.3420.1061-0.120.3842-0.3289-0.505-0.03360.18330.01990.0430.22360.01530.22484.2379-39.313341.2206
42.95120.85320.35793.006-0.79322.65050.1374-0.02570.2170.09720.11510.4607-0.1831-0.6313-0.20.2161-0.01740.07620.38610.03040.25171.8055-43.405448.5132
52.30090.263-0.12251.0315-0.2492.052-0.04270.1115-0.1039-0.0191-0.0569-0.01290.15760.06170.06530.1461-0.00620.0130.15360.01390.1813.942-46.343536.6027
62.87031.8242-0.39392.81650.33853.1767-0.10320.15220.0066-0.11630.0212-0.18310.03060.32410.14430.16620.04060.01370.29640.05150.198923.2455-43.272830.0409
71.28390.2694-0.7212.1683-0.37712.8770.01530.0986-0.04660.1071-0.1223-0.00260.02280.27150.07440.1376-0.0028-0.00180.20490.03410.174318.6708-42.824234.5514
83.19581.4407-0.64647.1134-2.13773.3645-0.03670.0081-0.22560.1105-0.1922-0.5789-0.120.30650.24030.15810.0037-0.01320.21060.03440.160321.4799-39.994336.7853
92.31360.1291-0.31943.44821.6144.56020.0411-0.0933-0.0952-0.0799-0.15320.56490.1141-0.64530.08470.1096-0.0092-0.01570.25160.04720.25364.7614-19.995419.279
105.1067-3.16710.67332.2009-0.34290.9987-0.4469-1.6175-0.39980.76540.62920.58120.0577-0.6274-0.00110.27360.0080.0630.5948-0.01330.313820.1445-13.204232.1072
113.2662-0.58710.99080.43650.38944.13050.29370.2396-0.2936-0.24190.0224-0.32490.15010.5168-0.3140.27350.0705-0.04080.2304-0.01520.244633.1435-23.770613.1127
123.5266-0.6636-0.47124.2727-0.42653.245-0.0008-0.0797-0.25920.12860.14350.52420.0648-0.3977-0.00190.137-0.0064-0.00340.23180.02450.19266.8338-21.088117.929
132.835-0.4392-0.43011.723-0.58162.94930.08980.2917-0.1205-0.1414-0.02580.15070.0731-0.42-0.01010.15730.0147-0.02560.21960.00950.160210.2981-19.30487.893
143.98230.05010.00351.08580.16281.42960.0502-0.27520.19150.088-0.0936-0.0607-0.08260.133-0.00490.15910.02190.01160.1401-0.00340.163318.8679-13.989220.5456
152.5468-0.9609-0.12722.0340.70963.0358-0.0261-0.47740.06190.06240.0669-0.0784-0.10360.260.07380.1536-0.0021-0.02940.2020.01550.191528.522-17.219322.8916
162.72730.72240.67381.38030.21650.51540.02210.0331-0.15660.0045-0.0754-0.1812-0.07720.11280.04770.1767-0.0179-0.0140.21160.05170.201925.3981-21.568818.0224
173.2342-0.2697-0.08914.08640.87682.95340.1482-0.20.19670.1161-0.0077-0.08690.02110.0287-0.12870.1436-0.019-0.0120.17770.02630.171523.4563-16.773617.6779
186.52850.65721.44816.5521-2.27241.8356-0.1276-0.7560.90660.92310.2470.4173-0.7206-0.9034-0.10850.32050.15680.08630.5458-0.02520.4707-1.9424-36.545843.5022
194.12530.7029-0.1972.0396-1.59291.2748-0.24150.941-0.0514-0.50650.13220.07290.0267-0.0806-0.04370.3021-0.0865-0.04990.44810.00420.24459.6799-47.149424.3598
205.88564.74261.83086.06491.48221.82670.30970.4730.10660.5233-0.5536-0.80060.42510.42390.46280.2652-0.01960.0340.30390.06810.371930.0264-40.209528.6735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 74 through 88 )
2X-RAY DIFFRACTION2chain 'D' and (resid 14 through 26 )
3X-RAY DIFFRACTION3chain 'D' and (resid 27 through 53 )
4X-RAY DIFFRACTION4chain 'D' and (resid 54 through 71 )
5X-RAY DIFFRACTION5chain 'D' and (resid 72 through 106 )
6X-RAY DIFFRACTION6chain 'D' and (resid 107 through 118 )
7X-RAY DIFFRACTION7chain 'D' and (resid 119 through 155 )
8X-RAY DIFFRACTION8chain 'D' and (resid 156 through 170 )
9X-RAY DIFFRACTION9chain 'A' and (resid 50 through 59 )
10X-RAY DIFFRACTION10chain 'A' and (resid 60 through 69 )
11X-RAY DIFFRACTION11chain 'A' and (resid 70 through 87 )
12X-RAY DIFFRACTION12chain 'B' and (resid 18 through 42 )
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 79 )
14X-RAY DIFFRACTION14chain 'B' and (resid 80 through 106 )
15X-RAY DIFFRACTION15chain 'B' and (resid 107 through 118 )
16X-RAY DIFFRACTION16chain 'B' and (resid 119 through 137 )
17X-RAY DIFFRACTION17chain 'B' and (resid 138 through 170 )
18X-RAY DIFFRACTION18chain 'C' and (resid 49 through 53 )
19X-RAY DIFFRACTION19chain 'C' and (resid 54 through 68 )
20X-RAY DIFFRACTION20chain 'C' and (resid 69 through 73 )

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