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- PDB-9qsp: Crystal structure of Zika Virus NS2B-NS3 protease in complex with... -

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Basic information

Entry
Database: PDB / ID: 9qsp
TitleCrystal structure of Zika Virus NS2B-NS3 protease in complex with Z2242050769
Components
  • Genome polyprotein
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / serine protease / bound fragment
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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / clathrin-dependent endocytosis of virus by host cell ...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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell cytoplasm / protein-macromolecule adaptor activity / methyltransferase cap1 activity / 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 / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / 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 / virion attachment to host cell / GTP binding / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding
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 NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor 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 / Immunoglobulin E-set / helicase superfamily c-terminal domain / 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: 1.4 Å
AuthorsBenz, L.S. / Becker, F. / Janssen, P. / Fuesser, F.T. / Weiss, M.S. / Kuemmel, D. / Koch, O.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO 4689/5-1 Germany
German Research Foundation (DFG)FE2166/1-1 Germany
German Research Foundation (DFG)GRK 2515 Germany
German Federal Ministry for Education and ResearchDZIF Flex Fund TTU 02.906 Germany
CitationJournal: To Be Published
Title: Accessing Ultralarge Chemical Spaces via a Sociable Fragment Library: Design and Crystallographic Screening
Authors: Janssen, P. / Becker, F. / Benz, L.S. / Fuesser, F.T. / Tolmachova, N. / Matviiuk, T. / Kondratov, I. / Weiss, M.S. / Kuemmel, D. / Koch, O.
History
DepositionApr 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: 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: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9073
Polymers24,7432
Non-polymers1641
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-26 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.920, 42.920, 215.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Components on special symmetry positions
IDModelComponents
11B-310-

HOH

21B-370-

HOH

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q32ZE1
#2: Protein Genome polyprotein


Mass: 18877.396 Da / Num. of mol.: 1 / Mutation: C143S, R107K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q32ZE1
#3: Chemical ChemComp-A1JAB / ~{N}-(2,2-dimethylpropyl)pyridin-2-amine


Mass: 164.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 24 % (w/v) PEG 2000, 0.1 M sodium acetate pH 4.6, 0.2 M ammonium sulfate

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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 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→42.92 Å / Num. obs: 41210 / % possible obs: 99.9 % / Redundancy: 11.16 % / CC1/2: 0.999 / Rrim(I) all: 0.08 / Net I/σ(I): 17.49
Reflection shellResolution: 1.4→1.48 Å / Mean I/σ(I) obs: 1.08 / Num. unique obs: 6533 / CC1/2: 0.434 / Rrim(I) all: 3.113 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→42.1 Å / SU ML: 0.1799 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.975
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2162 2061 5 %
Rwork0.1958 39144 -
obs0.1968 41205 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 12 97 1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01041487
X-RAY DIFFRACTIONf_angle_d1.11022019
X-RAY DIFFRACTIONf_chiral_restr0.0958220
X-RAY DIFFRACTIONf_plane_restr0.0097261
X-RAY DIFFRACTIONf_dihedral_angle_d6.4188216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.3281350.3382565X-RAY DIFFRACTION99.96
1.43-1.470.37311330.32172522X-RAY DIFFRACTION100
1.47-1.510.27921340.29642558X-RAY DIFFRACTION99.89
1.51-1.550.30871360.27292565X-RAY DIFFRACTION99.93
1.55-1.60.25641340.25472562X-RAY DIFFRACTION99.89
1.6-1.660.29011350.27442558X-RAY DIFFRACTION99.96
1.66-1.730.29461350.24382566X-RAY DIFFRACTION99.96
1.73-1.80.30051360.21442582X-RAY DIFFRACTION99.89
1.8-1.90.21891360.19812576X-RAY DIFFRACTION99.96
1.9-2.020.20841370.1932605X-RAY DIFFRACTION99.71
2.02-2.170.23131370.1912600X-RAY DIFFRACTION99.74
2.18-2.390.19241380.17062631X-RAY DIFFRACTION99.93
2.39-2.740.18331390.18792648X-RAY DIFFRACTION99.93
2.74-3.450.20761430.18352701X-RAY DIFFRACTION100
3.45-42.10.19181530.17522905X-RAY DIFFRACTION99.84
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)
14.88485411892-3.63674507767-4.316732398049.725310530161.45902723114.46782330338-0.1829914792850.179059247984-1.13591186732-0.216375120397-0.07821170134340.1703897698010.748584627160.1641987759370.2787325880660.276950013298-0.0462544724815-0.03346145193090.196990504991-0.05460222345830.358860270326-4.241751973913.1132334638413.2522498248
23.88178444941-3.87131636935-3.05631320934.278034516453.89186491974.094287812310.144739999273-0.08730988939350.02211782342-0.411484941891-0.2178106467380.35504215038-0.2221057966790.06226923896310.1377614855030.224325401492-0.01511630238570.01990464114190.216091428065-0.008803157660910.269710336416-9.7573445676513.76608830623.0464935759
32.7367387484-0.596381477841-0.4606083553584.90518954202-2.153464487477.133732197510.31255464606-2.95701592842-0.4686341277961.442637080810.04332494823010.4673218495840.425911612307-0.5688724010191.059087955160.37360611201-0.05747586291230.137895297630.702569022744-0.08746823225260.266456974377-5.6504911228323.244130762932.6369688378
45.806249600330.674903646294-4.246140110622.564399035131.2808309044.39034250856-0.047308447863-2.81622750357-1.12750649840.417906063022-0.293382239319-0.09292312943050.512567740234-0.5044737647670.09015951492350.407774728419-0.03611202840040.00434531140410.5887847841940.06419000724960.274765565735.2892900355822.612854673434.0338917084
54.408651892170.387216034005-0.4690949968673.968233812884.012875657919.203770275160.02181599253510.5210293074430.226489966924-0.1439666715910.268722440556-0.330307888214-0.3307808010750.438624470318-0.3010721106020.181162348981-0.02293242287410.01351711940950.2510945569340.022608049140.21895377198516.179354383625.178858644613.568047653
64.28582751851-5.43713089336-2.771911132548.622315905781.615240735226.468437169020.04122734739520.309942459633-0.648775947518-0.0867353410987-0.1199481452680.7507965565560.281419040513-0.3416639053870.07789849409780.175488626239-0.06405143312480.0259844438570.224374506242-0.01594606454390.263475223281-6.928279685179.598295162817.3214482008
76.85988859108-1.932914711690.3262469673230.907246485106-0.568777650044.05618343918-0.1109271031750.0742599350571-0.581836885667-0.06182839587970.003603218767990.03678362633710.6643778091910.06735583120850.1186869113390.258635785774-0.0341134074210.05493822960010.163075518606-0.01617005605780.223898097031-1.311603216216.3625404820515.6648068274
85.63138012411-0.8659455746461.021527295373.61900319385-0.4318233856765.17251463161-0.03766498383310.117372032495-0.0147458227071-0.0618047060776-0.0001319288520630.007499409307190.057692256534-0.12829990941-0.03679686979350.141271269381-0.02264035005590.02017855293060.149941249876-0.01137451285180.117007318004-1.1597749321714.81132136499.60701798478
94.87005982815-0.6154296260190.5621770625544.32492592579-0.9142672359395.47641292630.165873119460.293782725146-0.45322299045-0.06267807786010.06931795281610.4534059722080.749731334158-0.403582490274-0.05043953424870.274311506398-0.0724596287844-0.02533524359560.256010492806-0.05901260039790.193258043301-5.693424332199.547310663255.38609659774
102.113253211460.8950482731631.092279747552.767614117622.235140125153.956675076560.01867073820940.04347998996280.207112985049-0.00889889374148-0.1273062029540.179502349479-0.212438641774-0.2274423986460.102511084210.152690917401-0.008420237559260.0137483270150.1609754255360.02328069846340.155733696654-0.85559155103424.341862438312.4845545527
113.753995949771.95134817690.3132020629292.189066670331.580746245443.31540738160.0101761305153-0.305183957668-0.4431121704390.4562526976880.0179838783968-0.09870816499680.319274845489-0.00224796072831-0.01276576643330.207289589559-0.02703131064420.01889141619350.2562709425130.01078082627210.2278234364150.021271044844914.167207988626.9130901532
127.311558392420.92100532533-2.175224097424.168238857041.423207918486.837475329220.27531775562-0.4210775433380.2537991244850.161834815932-0.21270192701-0.0895022429896-0.329597676340.290727534391-0.05970437721350.1513679413720.0356632384817-0.02615697669290.1269807287180.003823186488780.1247253663017.3567699773626.375627926123.837993818
133.135251408150.5346002974880.2895088414483.874500618981.550699826381.054385081440.09526117771410.0871482594652-0.01140720796220.0594509451612-0.0441190226965-0.263623838705-0.2245512945350.1769318432340.008513004848610.211872706851-0.01748162492020.01155372476030.2073487160730.01617215604630.1465157476468.563676752321.035262435618.7949712817
143.85311896689-3.73091887872-2.808062469733.889014935392.891150076984.03083672131-0.0281906002431-0.568741721860.670128259640.5433422269070.08315595558860.0695781680135-0.197999203272-0.1003943960490.1190739100710.222790208896-0.02167945609460.05649414588250.225539695467-0.07136412384970.294010681101-4.4829834123926.612964108922.9995509185
157.302000703380.893024572730.03540260726154.738997463821.529837592913.4732747990.09805160235250.0133039493216-0.07899897507410.3147770913810.0159531126924-0.2721128402680.120791216520.2833955827290.01343168440320.16232753069-0.0380944650103-0.008244918133370.1203204507121.08157958823E-50.09938947594928.4608610543921.797482958317.4298492356
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 50 through 54 )AA50 - 541 - 5
22chain 'A' and (resid 55 through 59 )AA55 - 596 - 10
33chain 'A' and (resid 60 through 64 )AA60 - 6411 - 15
44chain 'A' and (resid 65 through 69 )AA65 - 6916 - 20
55chain 'A' and (resid 70 through 87 )AA70 - 8721 - 38
66chain 'B' and (resid 18 through 27 )BB18 - 271 - 10
77chain 'B' and (resid 28 through 42 )BB28 - 4211 - 23
88chain 'B' and (resid 43 through 53 )BB43 - 5324 - 34
99chain 'B' and (resid 54 through 71 )BB54 - 7135 - 52
1010chain 'B' and (resid 72 through 94 )BB72 - 9453 - 75
1111chain 'B' and (resid 95 through 106 )BB95 - 10676 - 87
1212chain 'B' and (resid 107 through 118 )BB107 - 11888 - 99
1313chain 'B' and (resid 119 through 137 )BB119 - 137100 - 118
1414chain 'B' and (resid 138 through 145 )BB138 - 145119 - 126
1515chain 'B' and (resid 146 through 170 )BB146 - 170127 - 151

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