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

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Basic information

Entry
Database: PDB / ID: 9rga
TitleCrystal structure of Zika NS2B-NS3 protease in complex with follow-up compound EOS87208 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: 1.38 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)49,7225
Polymers49,4864
Non-polymers2361
Water3,999222
1
A: Serine protease subunit NS2B
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9793
Polymers24,7432
Non-polymers2361
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-27 kcal/mol
Surface area9070 Å2
2
C: Serine protease subunit NS2B
D: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)24,7432
Polymers24,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-25 kcal/mol
Surface area10090 Å2
Unit cell
Length a, b, c (Å)59.820, 59.820, 214.120
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-A1JFZ / (3,5-dimethylfuran-2-yl)-[(2~{S})-2-(methylaminomethyl)pyrrolidin-1-yl]methanone


Mass: 236.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.94 Å3/Da / Density % sol: 36.61 %
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: 1.38→45.85 Å / Num. obs: 81054 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.08 / Net I/σ(I): 17.41
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.38-1.461.151128450.6211.2061
1.46-1.560.713121250.8490.7491
1.56-1.690.449113390.940.471
1.69-1.850.25104630.980.2621
1.85-2.070.13995340.9940.1461
2.07-2.390.08784620.9980.0911
2.39-2.920.06272020.9980.0651
2.92-4.130.03957060.9990.0411
4.13-45.850.03133780.9990.0321

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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: 1.38→41.5 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1901 2100 2.59 %
Rwork0.1779 --
obs0.1782 81048 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 17 222 3139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042999
X-RAY DIFFRACTIONf_angle_d0.8524068
X-RAY DIFFRACTIONf_dihedral_angle_d12.8861094
X-RAY DIFFRACTIONf_chiral_restr0.08447
X-RAY DIFFRACTIONf_plane_restr0.006531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.28861370.3065125X-RAY DIFFRACTION99
1.41-1.450.29691370.2685154X-RAY DIFFRACTION100
1.45-1.490.2771390.25185215X-RAY DIFFRACTION100
1.49-1.530.251370.23085171X-RAY DIFFRACTION100
1.53-1.580.24271380.22315181X-RAY DIFFRACTION100
1.58-1.640.2221380.21895194X-RAY DIFFRACTION100
1.64-1.70.22891390.20745219X-RAY DIFFRACTION100
1.7-1.780.211380.18985196X-RAY DIFFRACTION100
1.78-1.870.20511400.17795267X-RAY DIFFRACTION100
1.87-1.990.17021390.16835228X-RAY DIFFRACTION100
1.99-2.140.17671400.1695261X-RAY DIFFRACTION100
2.14-2.360.16161410.15875299X-RAY DIFFRACTION100
2.36-2.70.20831420.17265332X-RAY DIFFRACTION100
2.7-3.40.19081440.16595402X-RAY DIFFRACTION100
3.4-41.50.15741510.16035704X-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)
11.54281.1606-0.06232.54560.0561.41330.07910.05880.10250.0013-0.00750.3083-0.1102-0.3689-0.05680.14680.00820.00930.21510.02870.18342.395-42.442939.3448
27.23970.31212.67275.51351.49882.92020.10170.36210.31940.09170.00340.9734-0.1436-1.09420.13510.17180.00020.02940.49470.03480.2909-2.025-39.617445.4103
31.55430.2729-0.19750.8554-0.48142.17610.01740.046-0.10410.0491-0.0582-0.02880.05950.07960.01670.1145-0.0049-0.00360.13530.01860.150315.8298-43.525237.0221
42.47291.7995-0.6415.1653-0.76692.3024-0.02170.0436-0.07310.044-0.010.02250.03360.14770.03840.09130.0059-0.00040.13840.01950.114919.128-42.973535.517
54.74320.86230.09636.37532.60654.01360.0050.0101-0.17-0.12280.00130.295-0.0808-0.4428-0.02060.080.0160.01810.19310.0710.18094.9271-19.634319.3141
67.22-3.6677-1.03452.08230.30480.4058-0.8201-1.292-0.09571.21480.85010.3836-0.0994-0.4448-0.06740.31930.09860.03020.3989-0.02150.247520.4861-12.604731.8635
72.5023-0.6291-0.77321.58511.02795.31390.16020.3198-0.1514-0.1003-0.0004-0.23750.22650.5961-0.14150.17440.0568-0.0080.20120.00170.212633.6869-23.654112.8431
83.4485-0.2191-0.26434.3746-0.03824.35720.0191-0.0422-0.1167-0.20820.10150.4154-0.1469-0.3902-0.10380.10940.02680.00940.19770.04150.15186.4015-19.03219.124
92.1672-0.8241-0.34873.5525-0.21023.27240.00110.0365-0.1076-0.02930.07670.13920.0917-0.2995-0.07990.0930.0061-0.01350.15360.01910.133910.1968-20.675613.9187
102.7837-2.04-3.6315.38472.8345.9988-0.3563-0.1622-0.56350.05790.27711.02650.4847-0.91340.15940.1884-0.0339-0.02580.35720.04670.28891.9237-22.517210.2998
116.7058-1.0714-2.74063.0325-0.08623.875-0.03390.2419-0.0955-0.06170.10140.28430.0914-0.4401-0.08880.13850.0155-0.02970.23370.03680.14297.9217-16.99844.2342
122.0668-0.35630.33171.0853-0.30911.5766-0.0246-0.03890.108-0.00010.0107-0.0604-0.11290.01130.0020.10580.0259-0.00140.12780.00970.141818.4868-15.057316.9354
134.8412-0.801-0.1722.99620.98236.0611-0.0189-0.33240.14470.00880.0992-0.1966-0.05370.3871-0.03610.11110.018-0.03010.10070.0220.1328.6134-16.870522.4998
141.7736-0.40350.80482.1880.39970.54090.04860.21780.02-0.1146-0.0656-0.1284-0.08450.13940.0290.1281-0.0144-0.00060.18270.04590.1425.38-21.251517.7861
152.59163.47113.54975.05994.58874.9690.0392-0.3940.26990.2445-0.1764-0.1209-0.46320.06460.15120.17110.0060.00740.1774-0.0140.179820.6588-8.349522.5099
164.4052-0.4643-0.24434.09470.86563.26450.00540.0846-0.01360.00310.0589-0.04860.00480.06120.05780.0857-0.0017-0.01490.12790.00380.119424.3965-19.218615.4125
171.4266-0.5129-0.43581.89392.08194.8996-0.2038-0.13960.43790.27910.12610.4096-0.5509-0.65830.10530.22570.08640.03510.43650.03760.2943-1.7515-36.8540.434
183.4429-2.7329-1.41757.10082.02771.9039-0.025-0.0916-0.3151-0.32330.11530.47520.2312-0.11220.02270.1614-0.019-0.04740.24190.04260.22222.7761-47.454730.0111
192.0316-1.7236-0.7032.1255-0.29221.4469-0.33071.012-0.3771-1.24760.2590.18730.0799-0.29680.28840.3288-0.09380.02150.3863-0.08960.149912.8784-50.491720.7986
208.05254.08093.24425.47882.65058.0409-0.02020.69540.1674-0.35170.1535-0.1566-0.13720.3059-0.01130.160.03360.03510.28980.06240.257425.8694-40.096125.7419
215.3812-0.1549-0.90074.01930.31981.52940.2377-0.49290.58370.5089-0.2635-0.2982-0.3980.656-0.16230.2603-0.1365-0.03230.32470.02520.220327.5984-33.802844.7641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 13 through 53 )
2X-RAY DIFFRACTION2chain 'D' and (resid 54 through 62 )
3X-RAY DIFFRACTION3chain 'D' and (resid 63 through 137 )
4X-RAY DIFFRACTION4chain 'D' and (resid 138 through 171 )
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 59 )
6X-RAY DIFFRACTION6chain 'A' and (resid 60 through 69 )
7X-RAY DIFFRACTION7chain 'A' and (resid 70 through 88 )
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 27 )
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 53 )
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 62 )
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 106 )
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 118 )
14X-RAY DIFFRACTION14chain 'B' and (resid 119 through 137 )
15X-RAY DIFFRACTION15chain 'B' and (resid 138 through 145 )
16X-RAY DIFFRACTION16chain 'B' and (resid 146 through 170 )
17X-RAY DIFFRACTION17chain 'C' and (resid 50 through 54 )
18X-RAY DIFFRACTION18chain 'C' and (resid 55 through 59 )
19X-RAY DIFFRACTION19chain 'C' and (resid 60 through 64 )
20X-RAY DIFFRACTION20chain 'C' and (resid 65 through 74 )
21X-RAY DIFFRACTION21chain 'C' and (resid 75 through 88 )

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