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- PDB-9t4p: Dengue 2 Virus NS2B-NS3 protease fusion protein with crystal epit... -

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Basic information

Entry
Database: PDB / ID: 9t4p
TitleDengue 2 Virus NS2B-NS3 protease fusion protein with crystal epitope mutation K174Q
ComponentsSerine protease subunit NS2B,Serine protease NS3
KeywordsVIRAL PROTEIN / protease crystal epitopes
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / 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 / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / 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, 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesdengue virus type 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFairhead, M. / Ni, X. / Koekemoer, L. / MacLean, E.M. / Wright, N.D. / Bowesman-Jones, H. / Von Delft, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171399 United States
CitationJournal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Ni, X. / Koekemoer, L. / MacLean, E.M. / Wright, N.D. / Bowesman-Jones, H. / Von Delft, F.
History
DepositionOct 30, 2025Deposition site: PDBE / Processing site: PDBE
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: Serine protease subunit NS2B,Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)25,9491
Polymers25,9491
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.486, 45.2, 40.46
Angle α, β, γ (deg.)90, 109.108, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine protease subunit NS2B,Serine protease NS3 / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B / Flavivirin protease NS3 ...Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 25949.021 Da / Num. of mol.: 1 / Mutation: K174Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) dengue virus type 2 / Production host: Escherichia coli (E. coli)
References: UniProt: P14337, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: LFS Eco well C09 0.1M HEPES pH 7, 0.2M Lithium chloride, 20% w/v PEG 6000, 10% v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976269 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976269 Å / Relative weight: 1
ReflectionResolution: 1.95→42.15 Å / Num. obs: 15533 / % possible obs: 99.86 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 10
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 5242 / CC1/2: 0.357

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.105)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→42.148 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.276 / WRfactor Rwork: 0.208 / SU B: 8.807 / SU ML: 0.224 / Average fsc free: 0.922 / Average fsc work: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 800 5.15 %RANDOM
Rwork0.2257 14733 --
all0.229 ---
obs-15533 99.852 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.249 Å2-0 Å2-0.097 Å2
2--0.131 Å2-0 Å2
3---0.149 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 0 48 1531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121510
X-RAY DIFFRACTIONr_bond_other_d0.0060.0161439
X-RAY DIFFRACTIONr_angle_refined_deg2.721.8142035
X-RAY DIFFRACTIONr_angle_other_deg1.221.7723337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4045194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.34156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79810268
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1111061
X-RAY DIFFRACTIONr_chiral_restr0.1380.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021772
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02314
X-RAY DIFFRACTIONr_nbd_refined0.1790.2242
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1440.21333
X-RAY DIFFRACTIONr_nbtor_refined0.1560.2692
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0860.26
X-RAY DIFFRACTIONr_nbd_other0.1410.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.27
X-RAY DIFFRACTIONr_mcbond_it6.5754.864782
X-RAY DIFFRACTIONr_mcbond_other6.564.866782
X-RAY DIFFRACTIONr_mcangle_it8.5968.72974
X-RAY DIFFRACTIONr_mcangle_other8.5938.724975
X-RAY DIFFRACTIONr_scbond_it8.4895.623728
X-RAY DIFFRACTIONr_scbond_other8.4845.628729
X-RAY DIFFRACTIONr_scangle_it11.5739.9761061
X-RAY DIFFRACTIONr_scangle_other11.5689.981062
X-RAY DIFFRACTIONr_lrange_it13.653.0921567
X-RAY DIFFRACTIONr_lrange_other13.60453.1051566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.401520.45910620.45611170.8960.84599.73140.392
2.001-2.0550.413460.4210950.4211420.9010.85899.91240.358
2.055-2.1150.421660.37910080.38210740.850.8841000.324
2.115-2.180.337470.3739800.37110280.9420.88299.90270.328
2.18-2.2510.307490.30510010.30510510.9180.92299.90490.262
2.251-2.330.423780.3018900.319710.8680.92999.6910.262
2.33-2.4170.336230.2789280.2799520.9210.9499.8950.229
2.417-2.5160.336400.2688740.2719160.9270.95299.78170.227
2.516-2.6270.375420.2598360.2658790.9050.95599.88620.21
2.627-2.7550.266660.2167780.228450.9510.97299.88170.184
2.755-2.9030.287400.217550.2137950.9520.9761000.176
2.903-3.0780.297460.1967010.2027480.9410.97699.86630.174
3.078-3.290.282340.197040.1937380.9530.9771000.173
3.29-3.5510.316330.1846150.196520.9490.9899.38650.17
3.551-3.8880.296330.1895740.1956080.9450.97899.83550.186
3.888-4.3420.279310.1765520.1825830.9630.9821000.184
4.342-5.0050.223240.1594640.1634890.9730.98499.79550.18
5.005-6.1080.28210.2234030.2254240.9530.9721000.239
6.108-8.5490.249180.2043200.2073390.9550.97499.7050.231
8.549-42.1480.226110.211930.2112040.9760.9621000.262

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