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- PDB-7o2m: Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus i... -

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Basic information

Entry
Database: PDB / ID: 7o2m
TitleCrystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2289
Components(Genome polyprotein) x 2
KeywordsVIRAL PROTEIN / FLAVIVIRIN / SERINE PROTEASE / NS2B-NS3 / ZIKA VIRUS
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / serine-type endopeptidase activity ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-UZZ / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHuber, S. / Heine, A. / Steinmetzer, T.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Based Optimization and Characterization of Macrocyclic Zika Virus NS2B-NS3 Protease Inhibitors.
Authors: Huber, S. / Braun, N.J. / Schmacke, L.C. / Quek, J.P. / Murra, R. / Bender, D. / Hildt, E. / Luo, D. / Heine, A. / Steinmetzer, T.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6053
Polymers24,9032
Non-polymers7021
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-26 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.274, 42.274, 216.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11B-351-

HOH

21B-373-

HOH

31B-380-

HOH

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Components

#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
#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
#3: Chemical ChemComp-UZZ / 1-[(3~{S},6~{S},9~{S},19~{R})-3,6-bis(4-azanylbutyl)-2,5,8,12,15,18-hexakis(oxidanylidene)-9-(phenylmethyl)-1,4,7,11,14,17-hexazacyclotricos-19-yl]guanidine


Mass: 701.860 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H55N11O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate 0.2 M ammonium sulfate 18 % PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→43.22 Å / Num. obs: 15560 / % possible obs: 94.1 % / Redundancy: 7.92 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.999 / Rsym value: 0.075 / Net I/σ(I): 14.32
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 2.17 / Num. unique obs: 2250 / CC1/2: 0.93 / Rsym value: 0.44

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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: 1.9→39.37 Å / SU ML: 0.2277 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.0539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2506 777 5 %
Rwork0.1831 14758 -
obs0.1865 15535 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 50 109 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971494
X-RAY DIFFRACTIONf_angle_d0.99812032
X-RAY DIFFRACTIONf_chiral_restr0.0608225
X-RAY DIFFRACTIONf_plane_restr0.0066272
X-RAY DIFFRACTIONf_dihedral_angle_d14.2395881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.31241160.2642203X-RAY DIFFRACTION86.4
2.02-2.170.29381180.23362246X-RAY DIFFRACTION89.27
2.17-2.390.27631250.20982367X-RAY DIFFRACTION91.65
2.39-2.740.27561330.22312512X-RAY DIFFRACTION97.42
2.74-3.450.26921370.18272612X-RAY DIFFRACTION98.88
3.45-39.370.21381480.14922818X-RAY DIFFRACTION99.16
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)
14.882840145114.8430956657-4.884025374574.79942810456-4.840789155964.8818212835-0.0456587327292-0.186178587398-0.263553177597-0.07668889096-0.267207086643-0.4990767240260.1743388685190.4272511971020.3542438250140.4330402525970.1381330286730.005965325235390.312359865595-0.02942933375280.30947464644326.145274296-10.5593918646-18.1010570804
24.384966360020.660045854935-0.8464113697111.52165223588-1.474370693584.289553063680.1366332387360.2085085208270.11848274645-0.379187131677-0.1114871775190.1990345844860.21284602659-0.170395858095-0.02708475250830.3324126352020.136944143718-0.01677450739660.230102647558-0.02360169782330.269792061388.846382039325.86982513952-19.3633152047
37.823154199896.12800836878-2.855184042598.15105806468-3.750231000584.40090828550.750904133282-0.468189390117-0.3794716732310.438392176481-0.620446838588-0.2484875340290.08097667441250.908450505381-0.123283365480.2932591650190.0964327835562-0.007888614977880.394047438609-0.04790965227550.21898091697627.0533629664-8.83504332026-17.684015305
47.011919868253.260592370980.4238373926121.902028358971.115472921853.972319242330.166051761706-0.0183125322057-0.7460378115330.0461661301625-0.230724357271-0.3214031810720.595518242091-0.03166437220.08901710393460.3148842467630.0765840107179-0.004314682652420.249863004087-0.009697406390840.29217404432520.2276718161-12.6848945628-15.5923786968
53.595678572225.731375404460.07800458287729.682934345991.252289097086.946365360120.3380551283640.108741562637-0.2441270707010.0223301201791-0.410989659388-0.1900291211750.1356540695830.314779117401-0.04410313461880.234611551550.0793560903086-0.02144992383670.240795901307-0.01286947632980.19445705657822.0432109645-3.47567362322-10.1772046906
62.438387338540.511150825412-0.2555713584072.44409568442.891982210183.741283894090.296760594003-0.400152544047-0.4862185458360.2447479076980.21128379261-0.269838624540.8595713767060.270269745792-0.4154781328170.480569006390.0678978719152-0.131300533470.279926534240.02562682810070.31587533240126.2409222473-8.41378347996-5.70328223464
78.58252101328-1.81211300451-5.064966771161.94710802143-1.077675656349.514766018810.223860498048-0.3396493507560.130298254239-0.0222983230887-0.0671104535841-0.0440388960135-0.3514907868790.00940079864342-0.136775120660.2918643472690.0372985000196-0.05734492825550.266890803335-0.02880590616310.21507354001618.2435451103-0.33502363017-6.02264751727
87.34787902992-2.754180149814.705660580194.79188825995-4.126778317258.625947265870.1357671599080.4743086854520.4786546910560.0763578369141-0.367265489641-0.0634342510897-0.7373260886620.5034508003770.1874387180370.2822051981040.07036205893050.07361026296240.237516239330.0003453887013530.22162375228722.02054406649.24838797716-16.276547749
95.084803667383.519429650550.0356462255513.50741928094-1.435131059322.069617874560.2643135775590.505554578489-0.223696444864-0.344368423819-0.339478477142-0.345571794712-0.0815248669919-0.195317307692-0.002230074808050.3103554727250.180590455046-0.01507729968540.385635892675-0.02104448597360.20201396891418.1276796714-4.98494616213-26.4933171841
107.83292065197-3.7284561822-3.376040656626.710620561750.02513993494623.877211952170.3602688878930.5121076635450.170906251719-0.654502705213-0.2373510283410.128005149645-0.343036322799-0.133526680574-0.1694801387890.276178026580.115445211319-0.0790015304940.2836927517330.002539806423160.21999013772711.58888361527.29195786506-23.4535064126
113.21806423553-1.04962776320.01892324165365.66333351611-1.684439583320.8538948563760.1295567329320.07330319521830.221229625669-0.100687712772-0.1847409927080.127906252423-0.277459587661-0.3561806817440.1103079190270.2743160294180.126620843431-0.04217010709910.394514639065-0.02325323192480.22346577353310.56819204792.46079754423-17.7731182028
122.47520663324-2.406737767041.331644048639.1008901091-7.953185925767.807028468910.1243314683150.5566767206280.575705242121-0.534661598764-0.3015330349040.0601080349303-0.2801011161850.3204241019380.1737866177950.3427328650950.1037414877160.03546572349370.2730745447740.03622337146980.30268633707823.36117245867.67206141107-23.1052457318
137.233458657443.81480470456-2.778920491086.056364631430.3329118158442.080338450370.01636308474970.2494845541380.155222966854-0.177090082203-0.04344359315970.2647823243540.0680527462703-0.2451618866140.08598021832640.3162054214990.110829674404-0.06001379924390.2467738433080.008851293175560.20272013242911.02368444863.34782899757-16.5960914164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 87 )
3X-RAY DIFFRACTION3chain 'B' and (resid 17 through 27 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 42 )
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 53 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 71 )
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 106 )
10X-RAY DIFFRACTION10chain 'B' and (resid 107 through 118 )
11X-RAY DIFFRACTION11chain 'B' and (resid 119 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 145 )
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 170 )

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