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- PDB-6y3b: Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus i... -

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Basic information

Entry
Database: PDB / ID: 6y3b
TitleCrystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2110
Components(Genome polyprotein) x 2
KeywordsVIRAL PROTEIN / FLAVIVIRIN / SERINE PROTEASE / NS2B-NS3 / ZIKA VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Thrombin, subunit H - #120 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 / Trypsin-like serine proteases / 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 / Thrombin, subunit H / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-O7N / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsHuber, S. / Heine, A. / Steinmetzer, T.
CitationJournal: Chemmedchem / Year: 2020
Title: Structure-Based Macrocyclization of Substrate Analogue NS2B-NS3 Protease Inhibitors of Zika, West Nile and Dengue viruses.
Authors: Braun, N.J. / Quek, J.P. / Huber, S. / Kouretova, J. / Rogge, D. / Lang-Henkel, H. / Cheong, E.Z.K. / Chew, B.L.A. / Heine, A. / Luo, D. / Steinmetzer, T.
History
DepositionFeb 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7225
Polymers24,9032
Non-polymers8193
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-40 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.626, 60.493, 83.139
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Genome polyprotein


Mass: 5865.384 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Plasmid: bZiPro / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8XX12, UniProt: Q32ZE1*PLUS
#2: Protein Genome polyprotein


Mass: 19037.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Plasmid: bZiPro / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8XX12, UniProt: Q32ZE1*PLUS

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Non-polymers , 4 types, 132 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-O7N / 1-[(8~{R},15~{S},18~{S})-15,18-bis(4-azanylbutyl)-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine


Mass: 630.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50N10O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate 2.0 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 S 6M / Detector: PIXEL / Date: Apr 12, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.589→48.91 Å / Num. obs: 33699 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.07 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0431 / Rpim(I) all: 0.0192 / Rrim(I) all: 0.04733 / Net I/σ(I): 21.16
Reflection shellResolution: 1.589→1.69 Å / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5381 / CC1/2: 0.895 / Rrim(I) all: 0.529 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI

5gpi


Resolution: 1.59→48.91 Å / SU ML: 0.1023 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.7014
RfactorNum. reflection% reflection
Rfree0.1883 1684 5 %
Rwork0.1617 --
obs0.1631 33697 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.55 Å2
Refinement stepCycle: LAST / Resolution: 1.59→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 56 129 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711554
X-RAY DIFFRACTIONf_angle_d0.93412125
X-RAY DIFFRACTIONf_chiral_restr0.061238
X-RAY DIFFRACTIONf_plane_restr0.0054284
X-RAY DIFFRACTIONf_dihedral_angle_d16.9202917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.640.28081370.20762619X-RAY DIFFRACTION99.42
1.64-1.690.19581380.18572636X-RAY DIFFRACTION99.93
1.69-1.750.19261390.17412631X-RAY DIFFRACTION99.96
1.75-1.820.19611380.15892633X-RAY DIFFRACTION99.93
1.82-1.90.18621390.15692628X-RAY DIFFRACTION99.86
1.9-20.18941390.15072641X-RAY DIFFRACTION99.82
2-2.130.17841390.15652643X-RAY DIFFRACTION99.96
2.13-2.290.17751410.14482685X-RAY DIFFRACTION100
2.29-2.520.2171400.1652669X-RAY DIFFRACTION99.86
2.52-2.890.17091420.15912682X-RAY DIFFRACTION99.86
2.89-3.640.19011420.15472710X-RAY DIFFRACTION99.86
3.64-48.910.18341500.16892836X-RAY DIFFRACTION99.27
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)
17.568258272164.02985144879-4.870432919682.86943719006-2.132204494063.428981797560.04600880103460.207064787333-0.566313838629-0.4942948039420.0601216260384-0.1107699122071.233427078890.0827223830052-0.100248278450.3696507791860.0527819071326-0.08614587152310.171817430375-0.07485679671080.318897054212-3.73377493251-32.3488778533.8874232124
24.58201628952-5.60211026574-4.978329362626.885429269726.092541652935.41584902576-0.0956132889648-0.100934115893-0.431034252237-7.81451074768E-5-0.0951840585220.6590365621190.1137772650690.1249161880420.2389723291490.33814181007-0.0656364090202-0.02337420990230.2834885488310.07592545072970.294505952077-5.0274041386-28.792766637418.7208349484
31.200180538492.89233470917-2.322834794247.22087931176-5.918276960784.911186862740.668612895097-0.73823189057-0.7923771454681.21419804434-0.986381202661-0.994845796958-0.1642693503210.7762680143280.3344533483970.397352793622-0.0581680990833-0.115039497610.31375402520.08209832796190.3082091527532.42682317235-16.489959755326.3626855076
49.27917064465-3.039468345351.861166945032.681046706461.317470929792.71086162998-0.181386031299-0.2552118125140.2359576379920.3582746275040.14522121805-0.4799239385380.0514794238064-0.2082437267540.06656191616520.329972937815-0.0349590795252-0.01195107533880.213746945768-0.02932538991370.2626768008593.71225140293-0.76832627601715.384960984
57.502439613846.265175508435.515703739498.898496961466.03356984.63593270035-0.1587375198540.3462416015150.207691632526-0.04784357538980.1149724875190.146705204389-0.3015992682860.204417616320.1134064993720.2391111534060.00698220309296-0.007023013155980.2320007203550.03768185624910.216628026245-3.26451886017-2.961142255531.15870001066
65.459608724550.0242433294397-1.931080483046.764274938061.048454566167.089703332840.2061377576840.269783227881-0.538150889988-0.106031473644-0.0864551207319-0.08719436749690.4857133282220.07373943095330.07609190701770.1953719812230.020244015216-0.07518652992660.138675114964-0.02043974664370.186350406936-3.44494756093-28.94716710128.03681675026
71.934187037180.864404722981.519970673972.296463118890.9612224080622.949139634230.0794915118036-0.0418157759754-0.0719961389910.10010824976-0.0739319550370.2349435533020.115870341805-0.2743300606610.007635483007090.1469120335930.01296652227210.006262056723650.182060202183-0.002481691007120.207694271159-11.6148197277-19.80767915557.38379865787
81.05711242232-0.235216885186-0.1387776809733.382102070930.3443478653422.66606741956-0.0166509511552-0.05569063840990.02434809460040.295327742135-0.0269047185504-0.02236230738490.01663326900880.05726322806520.03416426228580.160649530188-0.0120069325545-0.004353026165280.174520091605-0.005973298223460.170116084188-0.891634429171-13.147794974715.0465262129
95.348532209161.064645969160.6339047189542.028754801990.3487953827152.48428504009-0.148680901065-0.4648508838110.1022226294670.02576133551040.04437706686290.3183603964050.00143258986583-0.1956667270510.1303587202420.1499948657430.005313451033330.01227254650480.1256745814380.000837644227340.184522055197-7.79519145876-10.71374677699.82498937044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 42 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 94 )
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 155 )
9X-RAY DIFFRACTION9chain 'B' and (resid 156 through 176 )

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