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- PDB-5tfo: CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE with a dele... -

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Basic information

Entry
Database: PDB / ID: 5tfo
TitleCRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE with a deletion V76-L86 in NS2b
ComponentsNS2B-NS3 Protease CHIMERA,NS2B-NS3 PROTEASE,NS2B-NS3 Protease CHIMERA
KeywordsVIRAL PROTEIN / Flavivirus / SERINE PROTEASE / 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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / clathrin-dependent endocytosis of virus by host cell ...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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / clathrin-dependent endocytosis of virus by host cell / protein-macromolecule adaptor activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell cytoplasm / methyltransferase cap1 activity / 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 / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / virion attachment to host cell / GTP binding / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / 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 ...Thrombin, subunit H - #120 / 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 superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / 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 / 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
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsAleshin, A.E. / Bankston, L. / Liddington, R.C.
CitationJournal: To Be Published
Title: A novel conformation for the Zika virus NS2B-NS3 protease offers new insights into biological regulation and inhibitor design.
Authors: Aleshin, A.E. / Bankston, L. / Shiryaev, S.A. / Terskikh, A. / Strongin, A. / Liddington, R.C.
History
DepositionSep 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS2B-NS3 Protease CHIMERA,NS2B-NS3 PROTEASE,NS2B-NS3 Protease CHIMERA
B: NS2B-NS3 Protease CHIMERA,NS2B-NS3 PROTEASE,NS2B-NS3 Protease CHIMERA


Theoretical massNumber of molelcules
Total (without water)49,0172
Polymers49,0172
Non-polymers00
Water41423
1
A: NS2B-NS3 Protease CHIMERA,NS2B-NS3 PROTEASE,NS2B-NS3 Protease CHIMERA


Theoretical massNumber of molelcules
Total (without water)24,5081
Polymers24,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS2B-NS3 Protease CHIMERA,NS2B-NS3 PROTEASE,NS2B-NS3 Protease CHIMERA


Theoretical massNumber of molelcules
Total (without water)24,5081
Polymers24,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.198, 55.198, 250.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NS2B-NS3 Protease CHIMERA,NS2B-NS3 PROTEASE,NS2B-NS3 Protease CHIMERA


Mass: 24508.318 Da / Num. of mol.: 2
Mutation: V76-L86 substituted with GG,V76-L86 substituted with GG,V76-L86 substituted with GG
Source method: isolated from a genetically manipulated source
Details: Residues V76-L86 of NS2B were substituted with GG Chains A and B were expressed as a single polypeptide chain.
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Plasmid: pGEX6P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q32ZE1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 36.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.51→39.03 Å / Num. obs: 13989 / % possible obs: 98.1 % / Redundancy: 6.3 % / CC1/2: 0.921 / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.2
Reflection shellResolution: 2.51→2.61 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.827 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ijo

2ijo


Resolution: 2.51→38.567 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.23
RfactorNum. reflection% reflection
Rfree0.2502 711 5.12 %
Rwork0.2176 --
obs0.2193 13874 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 89 Å2
Refinement stepCycle: LAST / Resolution: 2.51→38.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 0 23 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032495
X-RAY DIFFRACTIONf_angle_d0.4933382
X-RAY DIFFRACTIONf_dihedral_angle_d18.0111448
X-RAY DIFFRACTIONf_chiral_restr0.046367
X-RAY DIFFRACTIONf_plane_restr0.002436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5087-2.70240.4051210.36352345X-RAY DIFFRACTION90
2.7024-2.97430.34471350.31082599X-RAY DIFFRACTION99
2.9743-3.40440.28361400.27112662X-RAY DIFFRACTION100
3.4044-4.28830.251550.20552691X-RAY DIFFRACTION100
4.2883-38.57110.20981600.17842866X-RAY DIFFRACTION100
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)
13.07832.55382.53356.1080.62315.22070.0361-0.34020.00120.2201-0.0660.06290.51670.2629-0.07680.48520.06160.19830.61950.02760.6546-20.1907-1.3293-21.9267
28.9637-0.65430.56785.9651.57015.95060.20480.0597-0.55850.1962-0.09840.24970.9094-0.4721-0.00140.341-0.07880.00180.50230.01830.5484-30.3568-1.6465-28.7002
36.35170.43841.17983.36470.973.78880.0606-0.5868-0.09780.2533-0.10210.59440.2842-0.38030.0320.3759-0.03370.08590.5718-0.02570.5475-30.97866.3025-24.9857
46.1425.6031-0.1517.92670.80766.78320.1617-0.0728-0.2271-0.13820.1796-0.2110.01710.8621-0.44950.26890.0850.04210.6626-0.08530.4639-15.137710.1321-24.9159
54.4712.1192-0.49768.51440.28278.09110.0976-0.33010.6480.0682-0.0820.2611-0.3743-0.2939-0.01990.2068-0.01210.01170.5984-0.06020.5554-21.17412.5078-23.86
63.6922-2.3584-1.35784.86646.18148.82210.6317-0.45560.4453-1.79930.524-0.499-1.05261.2612-1.00720.9277-0.01150.1090.86050.03780.7731-17.00385.1296-55.2043
74.35230.67530.42956.9535.59648.30480.05270.01010.5061-0.62510.03370.4361-0.62960.1697-0.00040.6530.1704-0.00990.7322-0.020.6611-24.32987.3141-49.4094
85.4196-2.0814-1.07526.46872.29736.43550.12390.1344-0.4414-0.7283-0.13250.60450.4364-0.1610.09860.88870.0803-0.1280.7714-0.05090.5109-24.9706-0.4755-54.1033
95.92615.10382.23875.8013-1.03337.09840.99020.87030.96780.94040.63582.3886-0.6125-0.7155-1.83191.1242-0.14140.05921.1982-0.03931.6664-29.2025-20.7301-49.3694
105.13950.84510.47377.35822.61517.86840.2614-0.1128-0.6547-0.5505-0.40290.67031.5962-0.3362-0.07241.12430.2028-0.12870.6745-0.11380.662-22.4572-8.8295-54.0353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 50:68 )A50 - 68
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1016:1052 )A1016 - 1052
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1053:1103 )A1053 - 1103
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1104:1118 )A1104 - 1118
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1119:1158 )A1119 - 1158
6X-RAY DIFFRACTION6( CHAIN B AND RESID 49:64 )B49 - 64
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1016:1055 )B1016 - 1055
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1056:1113 )B1056 - 1113
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1114:1119 )B1114 - 1119
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1120:1157 )B1120 - 1157

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