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- PDB-7i9m: Group deposition of ZIKV NS2B-NS3 protease in complex with inhibi... -

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Basic information

Entry
Database: PDB / ID: 7i9m
TitleGroup deposition of ZIKV NS2B-NS3 protease in complex with inhibitors from ASAP Discovery Consortium -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0017733-001
Components
  • Serine protease NS3
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / SGC - Diamond I04-1 / XChemExplorer / ASAP Discovery Consortium
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host toll-like receptor signaling pathway ...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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / protein-macromolecule adaptor activity / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase activity / 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 / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / viral RNA genome replication / DNA clamp loader activity / serine-type endopeptidase activity / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / : / viral envelope / host cell nucleus / GTP binding / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 / 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 / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.86 Å
AuthorsNi, X. / Marples, P.G. / Godoy, A.S. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Fairhead, M. / Lithgo, R.M. / Lee, A. / Kenton, N. ...Ni, X. / Marples, P.G. / Godoy, A.S. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Fairhead, M. / Lithgo, R.M. / Lee, A. / Kenton, N. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Williams, E.P. / Chandran, A.V. / Walsh, M.A. / Fearon, D. / 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: Group deposition of ZIKV NS2B-NS3 protease in complex with inhibitors from ASAP Discovery Consortium
Authors: Ni, X. / Marples, P.G. / Godoy, A.S. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Fairhead, M. / Lithgo, R.M. / Lee, A. / Kenton, N. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. ...Authors: Ni, X. / Marples, P.G. / Godoy, A.S. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Fairhead, M. / Lithgo, R.M. / Lee, A. / Kenton, N. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Williams, E.P. / Chandran, A.V. / Walsh, M.A. / Fearon, D. / von Delft, F.
History
DepositionApr 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 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
B: Serine protease NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6874
Polymers23,1852
Non-polymers5022
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-27 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.530, 42.530, 218.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-334-

HOH

21B-358-

HOH

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Components

#1: Protein/peptide Serine protease subunit NS2B / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B


Mass: 5067.486 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 Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 18117.629 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-A1B86 / benzyl [3-({4-[(1R)-1-aminoethyl]phenyl}carbamoyl)-5-chlorophenyl]carbamate


Mass: 423.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22ClN3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.854→54.443 Å / Num. obs: 14741 / % possible obs: 92.5 % / Redundancy: 24.3 % / Biso Wilson estimate: 43.51 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.037 / Rrim(I) all: 0.183 / Net I/σ(I): 11.7 / Num. measured all: 357471
Reflection shell

Num. unique all: 737 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.854-1.97224.4179480.6560.6523.2441.467.2
5.745-54.44320.4150300.9950.0210.09329.3100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.4 (20-OCT-2021)refinement
Aimlessdata scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5GPI

5gpi


Resolution: 1.86→42.53 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.175 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 885 4.95 %RANDOM
Rwork0.2359 ---
obs0.2371 17894 99.9 %-
Displacement parametersBiso max: 115.62 Å2 / Biso mean: 59.47 Å2 / Biso min: 34.62 Å2
Baniso -1Baniso -2Baniso -3
1--5.3973 Å20 Å20 Å2
2---5.3973 Å20 Å2
3---10.7946 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 1.86→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 34 76 1586
Biso mean--86.18 60.76 -
Num. residues----195
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d536SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes294HARMONIC5
X-RAY DIFFRACTIONt_it1570HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion195SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1133SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1570HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2135HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion15.18
LS refinement shellResolution: 1.86→1.88 Å / Total num. of bins used: 45
RfactorNum. reflection% reflection
Rfree0.443 27 6.63 %
Rwork0.4234 380 -
all-407 -
obs--98.05 %
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)
14.1525-2.35950.13564.14791.16074.72380.60140.46710.3537-0.6378-0.4871-0.37940.0130.4452-0.1142-0.00860.21980.1464-0.07550.1106-0.2518-13.5203-1.4941-19.388
21.6159-1.63090.37751.81020.03012.54450.48450.1530.1856-0.2141-0.40470.02970.14550.2221-0.07970.07860.17880.03850.0020.043-0.0798-18.36561.0981-15.8137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A50 - 88
2X-RAY DIFFRACTION2{ B|* }B16 - 171

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