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

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Basic information

Entry
Database: PDB / ID: 7zvv
TitleCrystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2196
Components(Serine protease ...) x 2
KeywordsVIRAL PROTEIN / FLAVIVIRIN / SERINE PROTEASE / NS2B-NS3 / ZIKA VIRUS
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 / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / protein-macromolecule adaptor activity ...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 / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / protein-macromolecule adaptor activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / 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 / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis 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
3-cyano-L-phenylalanine / 4-cyano-L-phenylalanine / (2R)-6-azanyl-2-carbamimidamido-hexanoic acid / 2-[3-(aminomethyl)phenyl]ethanoic acid / 3-cyclohexyl-D-alanine / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHuber, S. / Steinmetzer, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch Pharm / Year: 2024
Title: Synthesis and structural characterization of new macrocyclic inhibitors of the Zika virus NS2B-NS3 protease.
Authors: Huber, S. / Braun, N.J. / Schmacke, L.C. / Murra, R. / Bender, D. / Hildt, E. / Heine, A. / Steinmetzer, T.
History
DepositionMay 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)25,8087
Polymers24,9032
Non-polymers9055
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.635, 60.645, 80.388
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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Serine protease ... , 2 types, 2 molecules AB

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


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: Q32ZE1
#2: Protein Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


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: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase

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Non-polymers , 6 types, 87 molecules

#3: Chemical ChemComp-V7T / (2R)-6-azanyl-2-carbamimidamido-hexanoic acid


Type: peptide-like / Mass: 188.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZAL / 3-cyclohexyl-D-alanine


Type: D-peptide linking / Mass: 171.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-V8N / 2-[3-(aminomethyl)phenyl]ethanoic acid


Type: peptide-like / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-4CF / 4-cyano-L-phenylalanine


Type: L-peptide linking / Mass: 190.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-3CF / 3-cyano-L-phenylalanine


Type: L-peptide linking / Mass: 190.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6 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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→48.41 Å / Num. obs: 25145 / % possible obs: 99.4 % / Redundancy: 7.15 % / Biso Wilson estimate: 31.78 Å2 / CC1/2: 1 / Rsym value: 0.033 / Net I/σ(I): 27.85
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.56 / Num. unique obs: 3950 / CC1/2: 0.959 / Rsym value: 0.47 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI

5gpi


Resolution: 1.75→33.51 Å / SU ML: 0.1917 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.4842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 1256 5 %
Rwork0.1868 23864 -
obs0.1886 25120 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.88 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 60 82 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491485
X-RAY DIFFRACTIONf_angle_d0.76842024
X-RAY DIFFRACTIONf_chiral_restr0.0574225
X-RAY DIFFRACTIONf_plane_restr0.0048284
X-RAY DIFFRACTIONf_dihedral_angle_d11.0482871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.32431320.25642540X-RAY DIFFRACTION97.55
1.82-1.90.26861380.23072619X-RAY DIFFRACTION99.24
1.9-20.25381380.21552614X-RAY DIFFRACTION99.39
2-2.120.2531390.20532628X-RAY DIFFRACTION99.68
2.12-2.290.24671380.20532632X-RAY DIFFRACTION99.28
2.29-2.520.27521400.21332648X-RAY DIFFRACTION99.5
2.52-2.880.23591400.20912672X-RAY DIFFRACTION99.72
2.88-3.630.22021420.20012692X-RAY DIFFRACTION99.82
3.63-33.510.18871490.15152819X-RAY DIFFRACTION99.4
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)
13.69747956399-5.284465226352.454570458348.18815561436-2.88738258574.707236902440.1308498186931.13949803197-0.805648947448-1.97794194189-0.0293725328879-0.8009003847211.45555366692-1.0893656761-0.167972241610.741990217316-0.03953367968810.1059515260130.426122494924-0.06253967581310.669618496041-7.06209651772-32.18129940512.68062409123
28.259755552712.81294210277-1.786496154793.712823336232.40238252133.99607257763-0.643846856032-0.0188027651914-0.8786376474110.7411390658990.4796325025070.6037833929572.13572853338-0.1813568481570.3740458199440.536922065547-0.04758564200570.09895179523630.5187364936730.1696279988510.499538511905-3.8217885549-30.053316265716.8851652801
39.053776427927.564489062254.54659887419.488075583636.34988566896.252138767110.830722025983-1.0617849302-0.6574967086281.2440365353-0.467696786827-0.9541370070710.7354070927941.19241749181-0.2985429266580.641358136602-0.00798350211077-0.03311168787510.6601745323410.0708097239270.278965254993-1.56919947557-19.308081772825.974373971
46.394830166491.68613948782-4.323608567414.24846986239-1.393043027938.34560726260.815179768648-2.49857561109-2.78992623813-0.2503904415-2.02891510888-0.05604172792371.606507783931.905441224011.028098866440.662550422602-0.151713284763-0.2243385477570.8833878533840.3779322267710.911166570146.68700904335-12.274528147924.2736081449
54.33420384945-2.755216577091.139763693014.06327828567-3.898551428026.87270769757-0.623447920202-0.4357015321330.7870824092080.615138169802-0.1044204580280.205913640124-1.28447731236-0.2774908171520.3866463846420.7105204310560.003129960944160.02934781337060.439053926036-0.2761592923120.6649741517011.9949944592-0.29959039515715.5852175217
65.77873205883-0.8854504762670.771552909950.260616115242-0.7618071062027.03454691613-0.298634804110.5818219121221.34818054783-0.8865670123740.812489823361.9823485107-0.724827748711-0.359789911286-0.01130707970860.474027154724-0.00938766056909-0.1805128343540.368091156270.2086083157670.865595112603-7.61883648105-2.383192516841.92346429428
78.02467131743-1.74675487448-3.618961691466.54898010541.384137351352.25137084537-0.411547995652-0.217644380074-0.9601836277440.210409114001-0.09562742217070.380810980330.890943501545-0.4890617924580.579391442910.386372108542-0.02898027576250.0382696655620.3033716800580.05362176243110.399693838153-6.91319516217-29.721541215611.2496009904
87.37710640848-0.4932837184260.9138388389648.322394724240.9648228342895.65350735607-0.1378372310820.133227603158-0.747120643829-0.52956238138-0.08620047879860.3847075579960.43719916629-0.1391070216090.2792393538060.324502309268-0.018267987561-0.00155436111960.2100477724240.004010857795870.311829170322-8.27183051249-24.53169980727.15226879135
95.842207434021.314118690641.86409379276.73561706178-3.455869900925.30835171390.115965477508-0.0524740281317-1.20984841692-0.411139386437-0.30759294028-0.3389977244460.620653029628-0.01086719525970.2491736921120.5730620895130.0175034540655-0.1092291298220.301191275942-0.04802591487930.708011071033-11.831512669-30.95278001833.59576281136
107.793187548632.88309558260.3981935885332.83819472861-3.071198344566.086101371060.1000043155060.1574942966650.193334200276-0.4755164074470.05753280961671.26185338140.435335119565-0.281068585976-0.1040368765810.337845547348-0.0441684462832-0.09067527142350.429784383636-0.022485227750.707558904045-19.0010478448-24.41524451535.28211429654
111.971938943-0.1951592374160.6792867695122.70178217565-3.621659484115.78380591778-0.0867462755889-0.1530441991591.13924717247-0.233589331332-0.07175172005892.07641306493-0.2782924283670.189983232056-0.1206653985170.3074150598710.0304564584842-0.08664428140240.3173461655470.001245019171610.66538093302-14.6513349533-16.1880501134.87551455212
120.5733275237930.08624950466841.125920912765.090688566721.310870490912.690782593840.57692661149-1.104319361590.5567832642861.28782072909-0.637329412551.106544698440.390282887649-0.4177585711480.1152943148940.434106508257-0.06173423416210.2067140039530.53481673946-0.1697750153770.548944757004-12.9258899709-12.582621358418.8314870524
135.61874894442-3.32905567281-2.116308289627.798607070494.945941304217.43823376440.191490995291-0.523382263730.1326064607950.0340725774451-0.0535187613931-1.03318116094-0.1314124761070.26295469401-0.1199574564040.318228761203-0.02449994229010.003565653746390.3472713753480.05668746083850.304882312612.25609504233-20.682786893615.5697814739
145.34993442362.185078934210.794807569364.73862131434-0.0820418747815.58770473592-0.111960918272-0.6451162606031.130097798520.901558609627-0.1537479531320.115905849253-0.44564010759-0.149074484810.1320139649110.366969924344-0.01051420603840.09353707491410.364774413403-0.1203505971930.373001567472-1.55195634997-6.9863534780816.9868361727
152.167415856942.057328641130.03788051374442.073225350941.014015965793.734557231560.0306328615335-0.1061388385360.6248592932230.230933529125-0.04971628076150.44869542686-0.0701237662158-0.08749767999730.01029158115990.2963106637410.01971274648980.03127385807990.287025706394-0.0149819221840.368103880278-2.85577046314-9.9700298003810.260871462
160.066930100807-0.1099880068980.4725855984960.389029709745-1.053403214782.962893720730.20529290894-1.226551403550.8562522113341.72039235884-0.78782995911.39646281363-0.1399348122830.123017851367-0.1441623754140.71459403702-0.06779189569990.3445562605410.618604935136-0.1512752329860.294050170755-7.71000640819-15.307379215223.1120045671
176.364879141142.51800908915-2.582093500826.74514107962-0.7267464354643.701940880790.217837854815-0.2002444635880.691728484269-0.00774058671418-0.01963880098920.4747054514670.01180829843860.0766733680965-0.2026786621830.275989868070.012139092023-0.001481919509050.290151821353-0.05155594111540.262756324029-4.74025945211-11.581733302110.2601978475
184.12617687584-0.2671229094270.3726929247163.936412680411.240567369833.76990408131-0.118667149434-0.1508940645150.725956023517-0.1124694863220.04848176344380.708849536226-0.117401264104-0.0834496158840.02566463930680.2462132217680.03763444086350.006886525751280.2076537823-0.05189017570720.345052423878-4.14617763676-8.490017540829.90429690026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 63 )
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 73 )
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 87 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 28 )
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 53 )
9X-RAY DIFFRACTION9chain 'B' and (resid 54 through 62 )
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 79 )
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 94 )
13X-RAY DIFFRACTION13chain 'B' and (resid 95 through 106 )
14X-RAY DIFFRACTION14chain 'B' and (resid 107 through 118 )
15X-RAY DIFFRACTION15chain 'B' and (resid 119 through 137 )
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 145 )
17X-RAY DIFFRACTION17chain 'B' and (resid 146 through 155 )
18X-RAY DIFFRACTION18chain 'B' and (resid 156 through 170 )

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