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- PDB-9rgf: Crystal structure of Zika NS2B-NS3 protease in complex with follo... -

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Basic information

Entry
Database: PDB / ID: 9rgf
TitleCrystal structure of Zika NS2B-NS3 protease in complex with follow-up compound EOS41783 from ECBL
Components
  • Genome polyprotein
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / crystallographic fragment screening / NS2B-NS3 Zika protease / ECBL-96 fragment library
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 / 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 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 / 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 / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / 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 superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / 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 / 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: 1.6 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
DepositionJun 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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: Genome polyprotein
C: Serine protease subunit NS2B
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7905
Polymers49,4864
Non-polymers3041
Water3,603200
1
A: Serine protease subunit NS2B
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)24,7432
Polymers24,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-26 kcal/mol
Surface area9070 Å2
2
C: Serine protease subunit NS2B
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0473
Polymers24,7432
Non-polymers3041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-26 kcal/mol
Surface area10220 Å2
Unit cell
Length a, b, c (Å)60.550, 60.550, 214.880
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 / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B


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: Q32ZE1
#2: Protein Genome polyprotein


Mass: 18877.396 Da / Num. of mol.: 2 / Mutation: C143S, R107K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q32ZE1
#3: Chemical ChemComp-A1JF3 / ~{N}-[(2~{S})-2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl)propyl]-5-methyl-furan-2-carboxamide


Mass: 304.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.99 Å3/Da / Density % sol: 38.35 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→46.24 Å / Num. obs: 53981 / % possible obs: 100 % / Redundancy: 11.27 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.107 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.71.1561.8485360.7211.207100
1.7-1.810.6580680.8850.679
1.81-1.960.38675530.9540.405
1.96-2.150.24169530.9840.251
2.15-2.40.1663290.9930.168
2.4-2.770.12156480.9960.127
2.77-3.390.07348090.9980.076
3.39-4.780.04938100.9990.052
4.78-46.240.0422750.9990.042

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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: 1.6→40.18 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2099 3.89 %
Rwork0.1809 --
obs0.1822 53977 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 21 200 3132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083019
X-RAY DIFFRACTIONf_angle_d0.9594096
X-RAY DIFFRACTIONf_dihedral_angle_d13.5731103
X-RAY DIFFRACTIONf_chiral_restr0.069450
X-RAY DIFFRACTIONf_plane_restr0.008537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.29421370.24813396X-RAY DIFFRACTION100
1.64-1.680.29491370.23643387X-RAY DIFFRACTION100
1.68-1.720.28341370.23563384X-RAY DIFFRACTION100
1.72-1.770.24251380.20873409X-RAY DIFFRACTION100
1.77-1.830.20041380.19143399X-RAY DIFFRACTION100
1.83-1.90.20331380.18143408X-RAY DIFFRACTION100
1.9-1.970.21761370.18193402X-RAY DIFFRACTION100
1.97-2.060.23481390.18323414X-RAY DIFFRACTION100
2.06-2.170.23761390.18313450X-RAY DIFFRACTION100
2.17-2.310.21041400.17433444X-RAY DIFFRACTION100
2.31-2.490.22451390.18233441X-RAY DIFFRACTION100
2.49-2.740.22221420.19853501X-RAY DIFFRACTION100
2.74-3.130.211410.19033502X-RAY DIFFRACTION100
3.13-3.940.20541440.16653558X-RAY DIFFRACTION100
3.94-40.180.19621530.16063783X-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)
18.64691.04962.50627.14263.35418.09550.1096-0.61770.70740.3205-0.1664-0.829-0.84290.08530.21770.1908-0.0275-00.1775-0.03720.215820.1091-8.71922.7102
23.9242-0.432-0.5573.69681.25322.47290.06970.06110.0485-0.1216-0.0153-0.09890.0680.12310.00670.1247-0.0166-0.02470.13310.02140.115124.4204-19.790615.7948
35.06960.431-0.25972.4788-1.02671.6414-0.16340.38140.0594-0.22890.20120.34170.0596-0.2306-0.14810.1597-0.0171-0.06210.23450.05320.18276.5525-44.342829.5457
42.07650.56230.21962.2526-0.093.31660.2787-0.31290.00550.1478-0.221-0.4364-0.19680.7645-0.06580.191-0.0845-0.00310.33510.05180.233528.3739-36.090340.1438
51.56261.4889-0.50571.4041-0.48530.160.02430.1279-0.1840.05590.04530.36490.1189-0.2374-0.0780.2019-0.0101-0.01260.2350.04430.294-1.1222-49.756536.6951
62.72660.51960.63582.22550.23033.90150.1376-0.13450.37860.1273-0.11670.4841-0.3953-0.43340.03740.17940.0290.05070.19610.00750.24464.2843-39.184141.2128
75.13191.7246-0.35685.48860.99033.41980.41950.03980.85880.18580.0470.8507-0.3301-1.0717-0.32680.29730.02820.1160.53770.06590.3694-1.9036-40.006145.9768
81.76471.2925-0.16132.623-0.70673.40080.118-0.1973-0.01380.2352-0.03990.0291-0.0815-0.2245-0.07650.1626-0.02290.02530.20070.02350.169.0306-44.466249.1935
92.58010.135-0.86971.2643-0.21462.4512-0.07730.1432-0.1569-0.1554-0.0674-0.11540.31050.12510.13570.1216-0.015-0.00250.13580.00250.164314.0056-47.444732.9827
101.81481.38220.85472.78061.0173.0772-0.21510.0447-0.2078-0.10650.0354-0.24540.08870.39220.05080.14560.04070.01740.27450.05980.176723.1609-43.37629.9272
112.22480.5141-0.59152.58970.20612.4871-0.0090.1211-0.07440.0566-0.0735-0.00180.11870.17810.02040.12010.00270.00110.15520.03230.128618.634-42.861634.4584
123.08061.5699-0.80623.8565-0.36072.37860.115-0.1249-0.17930.1663-0.187-0.01750.0130.26050.13160.11710.0015-0.00120.15250.02580.102921.0369-41.246937.6031
132.21290.18950.14776.60594.17877.49-0.06810.0406-0.1910.00410.05390.44660.0102-0.4103-0.02170.0788-0.0151-0.00070.22210.04520.25684.6105-20.080219.0651
146.7044-6.35110.70536.2271-1.0360.7249-0.6809-1.4567-0.1690.84810.99310.52160.0004-0.4035-0.13350.27190.02580.05090.5245-0.0440.274319.8589-13.371932.0944
152.8116-0.82120.37431.96440.04564.46640.30880.1622-0.1143-0.1699-0.1032-0.37540.16770.5224-0.1250.19520.0461-0.00770.26280.02490.231133.7037-23.891213.2711
162.5247-0.8544-0.61222.5512-0.68383.9377-0.01860.0883-0.19710.06110.02280.25150.0857-0.3302-0.03550.0892-0.0073-0.01780.1420.00170.14138.799-20.265915.1837
172.4821-0.0497-1.31522.4775-1.09793.88740.07730.1695-0.1029-0.01790.00320.29120.1537-0.7289-0.07240.1999-0.0214-0.05970.3306-0.00260.21345.369-19.81436.5933
182.2611-0.11620.99940.97320.13842.0865-0.01920.14580.1847-0.1039-0.041-0.0651-0.14680.0480.05850.15130.00110.00410.16420.04620.168619.5896-12.96311.2508
195.41461.9701-0.27874.68830.43891.31640.095-0.8497-0.30080.378-0.20290.13670.13980.220.07310.15830.02890.01730.25070.02220.147315.7459-19.669727.3998
203.9563-1.1170.00522.90791.15184.60830.0083-0.39010.07570.03220.0191-0.114-0.11920.28190.0150.1031-0.0077-0.02470.15470.01460.114928.2631-17.180123.0057
211.5634-0.16660.9961.49140.0440.64740.00430.05350.0376-0.0844-0.1065-0.1775-0.05440.26380.08340.1547-0.0163-0.00090.20250.0540.158924.8203-21.754718.1666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 138 through 145 )
2X-RAY DIFFRACTION2chain 'B' and (resid 146 through 170 )
3X-RAY DIFFRACTION3chain 'C' and (resid 49 through 68 )
4X-RAY DIFFRACTION4chain 'C' and (resid 69 through 88 )
5X-RAY DIFFRACTION5chain 'D' and (resid 14 through 26 )
6X-RAY DIFFRACTION6chain 'D' and (resid 27 through 53 )
7X-RAY DIFFRACTION7chain 'D' and (resid 54 through 62 )
8X-RAY DIFFRACTION8chain 'D' and (resid 63 through 79 )
9X-RAY DIFFRACTION9chain 'D' and (resid 80 through 106 )
10X-RAY DIFFRACTION10chain 'D' and (resid 107 through 118 )
11X-RAY DIFFRACTION11chain 'D' and (resid 119 through 155 )
12X-RAY DIFFRACTION12chain 'D' and (resid 156 through 171 )
13X-RAY DIFFRACTION13chain 'A' and (resid 50 through 59 )
14X-RAY DIFFRACTION14chain 'A' and (resid 60 through 69 )
15X-RAY DIFFRACTION15chain 'A' and (resid 70 through 88 )
16X-RAY DIFFRACTION16chain 'B' and (resid 18 through 53 )
17X-RAY DIFFRACTION17chain 'B' and (resid 54 through 71 )
18X-RAY DIFFRACTION18chain 'B' and (resid 72 through 93 )
19X-RAY DIFFRACTION19chain 'B' and (resid 94 through 106 )
20X-RAY DIFFRACTION20chain 'B' and (resid 107 through 118 )
21X-RAY DIFFRACTION21chain 'B' and (resid 119 through 137 )

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