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- PDB-7zld: Crystal Structure of Unlinked NS2B_NS3 Protease from Zika Virus i... -

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Basic information

Entry
Database: PDB / ID: 7zld
TitleCrystal Structure of Unlinked NS2B_NS3 Protease from Zika Virus in Complex with Inhibitor MI-2223
Components
  • Serine protease NS3
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / FLAVIVIRIN / SERINE PROTEASE / NS2B-NS3 / ZIKA VIRUS
Function / homology
Function and homology information


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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / 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 ...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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / 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 / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell nucleus / GTP binding / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / 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 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / : / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-IY3 / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsHuber, S. / Steinmetzer, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch Pharm / Year: 2023
Title: Thermodynamic characterization of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its acyclic analogs.
Authors: Hammerschmidt, S.J. / Huber, S. / Braun, N.J. / Lander, M. / Steinmetzer, T. / Kersten, C.
History
DepositionApr 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 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: Serine protease subunit NS2B
B: Serine protease NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4943
Polymers24,9032
Non-polymers5911
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.390, 42.390, 216.404
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-379-

HOH

21B-385-

HOH

31B-400-

HOH

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Components

#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
#3: Chemical ChemComp-IY3 / (2~{S})-2-[2-[3-(aminomethyl)phenyl]ethanoylamino]-6-azanyl-~{N}-[(2~{S})-6-azanyl-1-[[(5~{R})-6-azanyl-5-carbamimidamido-6-oxidanylidene-hexyl]amino]-1-oxidanylidene-hexan-2-yl]hexanamide


Mass: 590.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H50N10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate 0.2 M ammonium sulfate 19 % PEG2000 macroseeding was performed to obtain larger crystal

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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 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.61→42.39 Å / Num. obs: 26714 / % possible obs: 99.3 % / Redundancy: 12.7 % / Biso Wilson estimate: 27.19 Å2 / CC1/2: 1 / Rsym value: 0.035 / Net I/σ(I): 34.32
Reflection shellResolution: 1.61→1.71 Å / Mean I/σ(I) obs: 5.07 / Num. unique obs: 4169 / CC1/2: 0.992 / Rsym value: 0.499

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI

5gpi


Resolution: 1.61→42.39 Å / SU ML: 0.2129 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.947
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 1332 5 %
Rwork0.1858 25307 -
obs0.1869 26639 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.17 Å2
Refinement stepCycle: LAST / Resolution: 1.61→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 42 134 1591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471508
X-RAY DIFFRACTIONf_angle_d0.77092056
X-RAY DIFFRACTIONf_chiral_restr0.055229
X-RAY DIFFRACTIONf_plane_restr0.0055277
X-RAY DIFFRACTIONf_dihedral_angle_d11.2116541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.670.35611250.29392423X-RAY DIFFRACTION97.1
1.67-1.730.25551290.24252417X-RAY DIFFRACTION98.19
1.73-1.810.26721310.19852478X-RAY DIFFRACTION98.75
1.81-1.910.19871290.19642472X-RAY DIFFRACTION98.78
1.91-2.030.22751320.19882498X-RAY DIFFRACTION98.72
2.03-2.180.21281320.20372511X-RAY DIFFRACTION99.62
2.18-2.40.22411340.19142528X-RAY DIFFRACTION99.51
2.4-2.750.25621340.21222565X-RAY DIFFRACTION99.85
2.75-3.470.21351380.18922615X-RAY DIFFRACTION99.85
3.47-42.390.17521480.16072800X-RAY DIFFRACTION99.26
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)
10.2388693037790.0511834387698-0.04233094471480.105240023991-0.01961981454440.0298750781174-0.1139641068690.282699817564-0.790335044152-0.188262373662-0.387538697610.2520916795380.383223251042-0.149647000266-0.006871506140160.5867504318920.071294914437-0.01098924749560.241935343315-0.00784608590740.4197395451763.36678314715.5554158135-13.3870216783
20.04542118850950.0505637164706-0.01212528382170.0643674587939-0.03150095112080.0404776444008-0.04338706955850.207023721556-0.1473530341080.09052669675250.169561826867-0.50524114105-0.204033157039-0.0173771758634-6.51965052973E-50.361958600280.1054195690110.05965924100460.31591692604-0.009478386980140.3301632903837.5054384284816.1591870732-24.0083953061
33.143248990320.682786773472-0.7131525671161.30083606521-0.6755065271440.3973687925370.01052729373211.13721020811-0.559968710753-0.931575091529-0.1505659458430.1016217154650.528399680583-0.0381445685678-0.1545822565120.6696612046790.2186844450210.08907202849080.485402366532-0.006022896826550.32309279257-2.2683399549224.8527436151-32.6292965698
40.541291686407-0.0671342389881-0.08924822261090.2657949197570.06077600806980.0960373670496-0.078191030237-0.09725894125590.0565059502265-0.1013330733170.09923608240450.198382732999-0.0722628077412-0.5271298703620.0004916953187250.3555865581180.0777666637009-0.0009826920661110.4352434307850.01147766606590.355964178178-16.265897621627.6684609825-12.7335460509
50.00628842147928-0.0130925920329-0.009597365516550.0259719995310.01936734749380.0143492672991-0.1895230822130.2735977653190.0699755269745-0.02193282800040.3922427668640.7397049782130.172479787433-0.5944824396760.02757663721950.2305936457210.05698821445250.03985290964310.5401647949750.08599554469190.430516057992-21.005064419327.2008941193-11.1544354239
60.515259527655-0.2416427173610.06137676326280.1894014011750.2633350193551.106972214060.1086870866230.0826803022819-0.2227741863550.0372303253782-0.0902958541607-0.1653144315240.282705034870.3228906834590.02848861422730.3588455832260.0384493989163-0.009696113872020.209992360632-0.01303055765120.2752113789572.517040368569.82725376198-16.6271608904
70.7847215758460.3592231072210.9043392366030.5629392691390.661691333161.538859037830.196511651827-0.192585229427-0.01811046810060.112709905945-0.0252760386689-0.1344038141450.1177895312110.007113715717250.004075256782160.2684677437780.0214201243237-0.0243732732680.1842742378570.01444342106950.2469639103571.9815339353415.8277453021-7.19149174847
82.29708283739-0.786421043688-0.2821960260311.25821472393-0.5512605745181.237112337870.2057166832960.2405922293380.0757112683382-0.317668922462-0.122984401927-0.0502410845097-0.191673243881-0.1335915995590.01077107604260.328252857480.08902174705930.01302028511080.2022443092930.015563401710.23329351437-3.1002695923725.2301382092-21.5286644548
91.00514977349-0.0316470232323-0.819743086141.41391293346-1.225547505921.777508468060.1361550221680.108233681481-0.00905262074058-0.24919922781-0.0693411332452-0.0408881456044-0.0880766614306-0.3038648890370.002300203459940.2772487268360.0524438154257-0.02265102772620.215716989501-0.006672123842040.225080908148-7.6952637568124.6737974888-17.9299044181
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 50 through 54 )AA50 - 541 - 5
22chain 'A' and (resid 55 through 59 )AA55 - 596 - 10
33chain 'A' and (resid 60 through 69 )AA60 - 6911 - 20
44chain 'A' and (resid 70 through 83 )AA70 - 8321 - 34
55chain 'A' and (resid 84 through 88 )AA84 - 8835 - 39
66chain 'B' and (resid 17 through 42 )BB17 - 421 - 26
77chain 'B' and (resid 43 through 79 )BB43 - 7927 - 63
88chain 'B' and (resid 80 through 118 )BB80 - 11864 - 102
99chain 'B' and (resid 119 through 171 )BB119 - 171103 - 155

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