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- PDB-7vxx: Zika virus NS2B/NS3 protease bZipro(C143S) in complex with 4-amin... -

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Basic information

Entry
Database: PDB / ID: 7vxx
TitleZika virus NS2B/NS3 protease bZipro(C143S) in complex with 4-amino benzamidine
Components
  • Serine protease NS3
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / ZIKV / NS2B/NS3 protease / inhibitor / complex
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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / 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 capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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 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 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 / : / Flavivirus NS3 helicase, C-terminal helical domain / 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
P-AMINO BENZAMIDINE / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsXiong, Y.C. / Cheng, F. / Zhang, J.Y. / Su, H.X. / Hu, H.C. / Zou, Y. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Chem. / Year: 2022
Title: Structure-based design of a novel inhibitor of the ZIKA virus NS2B/NS3 protease.
Authors: Xiong, Y. / Cheng, F. / Zhang, J. / Su, H. / Hu, H. / Zou, Y. / Li, M. / Xu, Y.
History
DepositionNov 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Serine protease NS3
C: Serine protease subunit NS2B
D: Serine protease NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7165
Polymers51,5804
Non-polymers1361
Water97354
1
A: Serine protease subunit NS2B
B: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)25,7902
Polymers25,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-26 kcal/mol
Surface area8270 Å2
MethodPISA
2
C: Serine protease subunit NS2B
D: Serine protease NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9263
Polymers25,7902
Non-polymers1361
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-26 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.149, 59.149, 214.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serine protease subunit NS2B


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: H8XX12
#2: Protein Serine protease NS3


Mass: 19924.557 Da / Num. of mol.: 2 / Mutation: C143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: H8XX12, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Chemical ChemComp-PBZ / P-AMINO BENZAMIDINE


Mass: 136.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.82 Å3/Da / Density % sol: 32.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 30% polyethylene glycol monomethyl ether 2000, 0.1M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.9→19.85 Å / Num. obs: 31118 / % possible obs: 99.9 % / Redundancy: 23.9 % / CC1/2: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.021 / Rrim(I) all: 0.103 / Net I/σ(I): 19.2 / Num. measured all: 743617
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9424.51.5924977920290.9090.3261.6262.6100
8.91-19.8520.30.037717035410.0080.03856.191.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.43 Å45.56 Å
Translation5.43 Å45.56 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LC0

5lc0


Resolution: 1.9→19.85 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1515 4.89 %
Rwork0.2034 29473 -
obs0.2052 30988 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.25 Å2 / Biso mean: 38.3071 Å2 / Biso min: 19.89 Å2
Refinement stepCycle: final / Resolution: 1.9→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 10 54 2674
Biso mean--47.01 40.53 -
Num. residues----369
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.960.26841320.239125862718
1.96-2.030.30971360.228326462782
2.03-2.110.28361180.219826462764
2.11-2.210.27421460.208526072753
2.21-2.320.22691340.202326382772
2.33-2.470.27431410.215726452786
2.47-2.660.2971380.225826342772
2.66-2.930.24711360.217626972833
2.93-3.350.2461530.205726892842
3.35-4.210.24071410.185427572898
4.21-19.850.19851400.196929283068
Refinement TLS params.Method: refined / Origin x: -30.4042 Å / Origin y: 16.1979 Å / Origin z: -26.8624 Å
111213212223313233
T0.1978 Å20.0021 Å2-0.026 Å2-0.1743 Å2-0.0051 Å2--0.192 Å2
L0.459 °20.081 °20.416 °2-0.0208 °20.0424 °2--0.5892 °2
S-0.0025 Å °0.0452 Å °-0.0227 Å °-0.0197 Å °0.0089 Å °0.0019 Å °0.0262 Å °0.0441 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allE201
2X-RAY DIFFRACTION1allA51 - 88
3X-RAY DIFFRACTION1allB18 - 168
4X-RAY DIFFRACTION1allC51 - 87
5X-RAY DIFFRACTION1allD13 - 170
6X-RAY DIFFRACTION1allS1 - 54

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