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- PDB-5lc0: Crystal structure of Zika virus NS2B-NS3 protease in complex with... -

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Basic information

Entry
Database: PDB / ID: 5lc0
TitleCrystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor
ComponentsNS2B-NS3 protease,NS2B-NS3 protease
KeywordsHYDROLASE / zika virus NS2B-NS3 protease / antiviral agents / boronic-acid inhibitor / cyclic diester with glycerol
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / 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 capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-6T8 / Core protein / Core protein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLei, J. / Hansen, G. / Zhang, L.L. / Hilgenfeld, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Center for Infection Research (DZIF)#TTU01.911_0 Germany
CitationJournal: Science / Year: 2016
Title: Crystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor.
Authors: Lei, J. / Hansen, G. / Nitsche, C. / Klein, C.D. / Zhang, L. / Hilgenfeld, R.
History
DepositionJun 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Aug 10, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS2B-NS3 protease,NS2B-NS3 protease
B: NS2B-NS3 protease,NS2B-NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4874
Polymers48,4662
Non-polymers1,0212
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-11 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.808, 125.808, 73.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NS2B-NS3 protease,NS2B-NS3 protease


Mass: 24233.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: BeH823339 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140FB25, UniProt: A0A140DLX4
#2: Chemical ChemComp-6T8 / N-((S)-3-(4-(aminomethyl)phenyl)-1-(((R)-4-guanidino-1-(5-hydroxy-1,3,2-dioxaborinan-2-yl)butyl)amino)-1-oxopropan-2-yl)benzamide


Mass: 510.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H35BN6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 3.47 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.5 M lithium sulfate monohydrate, 0.1 M sodium acetate trihydrate, pH 4.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.435
11-h,-k,l20.565
ReflectionResolution: 2.7→73.46 Å / Num. obs: 18733 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YOL

2yol


Resolution: 2.7→62.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.792 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.063 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26332 902 4.8 %RANDOM
Rwork0.20379 ---
obs0.20665 17810 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.519 Å2
Baniso -1Baniso -2Baniso -3
1--50.14 Å2-0 Å2-0 Å2
2---50.14 Å2-0 Å2
3---100.28 Å2
Refinement stepCycle: 1 / Resolution: 2.7→62.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 74 15 2981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193030
X-RAY DIFFRACTIONr_bond_other_d0.0020.022841
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9824104
X-RAY DIFFRACTIONr_angle_other_deg1.13436534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7825379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53424.194124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.1515475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9121518
X-RAY DIFFRACTIONr_chiral_restr0.140.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213445
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02685
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.3869.2341528
X-RAY DIFFRACTIONr_mcbond_other6.3839.2351527
X-RAY DIFFRACTIONr_mcangle_it9.39313.8461903
X-RAY DIFFRACTIONr_mcangle_other9.39213.8451904
X-RAY DIFFRACTIONr_scbond_it6.0889.531501
X-RAY DIFFRACTIONr_scbond_other6.0869.531502
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.02914.1382201
X-RAY DIFFRACTIONr_long_range_B_refined12.88274.1263433
X-RAY DIFFRACTIONr_long_range_B_other12.88174.1313434
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 60 -
Rwork0.343 1299 -
obs--99.93 %

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