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- PDB-5t1v: Crystal structure of Zika virus NS2B-NS3 protease in apo-form. -

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Basic information

Entry
Database: PDB / ID: 5t1v
TitleCrystal structure of Zika virus NS2B-NS3 protease in apo-form.
ComponentsNS2B-NS3 protease,NS2B-NS3 protease
KeywordsHYDROLASE / Peptidase S7 / Flavivirus NS3 serine protease. / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / symbiont-mediated suppression of host toll-like receptor signaling pathway ...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 / symbiont-mediated suppression of host toll-like receptor signaling pathway / protein-macromolecule adaptor activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / 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 / lipid binding / viral envelope / 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
Thrombin, subunit H - #120 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 / 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: 3.1 Å
AuthorsNocadello, S. / Light, S.H. / Minasov, G. / Shuvalova, L. / Cardona-Correa, A.A. / Ojeda, I. / Vargas, J. / Johnson, M.E. / Lee, H. / Anderson, W.F. ...Nocadello, S. / Light, S.H. / Minasov, G. / Shuvalova, L. / Cardona-Correa, A.A. / Ojeda, I. / Vargas, J. / Johnson, M.E. / Lee, H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of Zika virus NS2B-NS3 protease in apo-form.
Authors: Nocadello, S. / Light, S.H. / Minasov, G. / Shuvalova, L.A. / Cardona-Correa, A.A. / Ojeda, I. / Vargas, J. / Johnson, M.E. / Lee, H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases
History
DepositionAug 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS2B-NS3 protease,NS2B-NS3 protease
B: NS2B-NS3 protease,NS2B-NS3 protease


Theoretical massNumber of molelcules
Total (without water)58,1462
Polymers58,1462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.086, 55.086, 249.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 6 - 222 / Label seq-ID: 27 - 243

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein NS2B-NS3 protease,NS2B-NS3 protease


Mass: 29072.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase

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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: 1.63 Å3/Da / Density % sol: 24.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 12.8mg/ml, 1M Sodium chloride, 0.05M Tris-HCl pH=8.5; Scrren: Classics II (H3), 0.24M Sodium malonate pH=7.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2016 / Details: C(111)
RadiationMonochromator: berrylium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 7675 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 79.3 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 17.8
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.74 / CC1/2: 0.925 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-5LC0

5lc0


Resolution: 3.1→29.9 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.881 / SU B: 51.041 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.55 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28755 739 9.7 %RANDOM
Rwork0.22263 ---
obs0.22862 6875 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.348 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å2-0 Å2-0 Å2
2--3.67 Å2-0 Å2
3----7.34 Å2
Refinement stepCycle: 1 / Resolution: 3.1→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 0 0 2442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192491
X-RAY DIFFRACTIONr_bond_other_d0.0010.022375
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9583376
X-RAY DIFFRACTIONr_angle_other_deg0.82435457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.585316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.10823.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.94715406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.3051518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212818
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02548
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5836.3511279
X-RAY DIFFRACTIONr_mcbond_other1.5836.3481278
X-RAY DIFFRACTIONr_mcangle_it2.8179.5061590
X-RAY DIFFRACTIONr_mcangle_other2.8169.511591
X-RAY DIFFRACTIONr_scbond_it1.2126.4821212
X-RAY DIFFRACTIONr_scbond_other1.2126.4851213
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1349.6461787
X-RAY DIFFRACTIONr_long_range_B_refined4.83973.4492722
X-RAY DIFFRACTIONr_long_range_B_other4.8473.3642720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8526 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 41 -
Rwork0.305 483 -
obs--100 %
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)
14.6969-4.789-3.54879.84397.08246.0247-0.1261-0.21030.2807-0.40590.3281-0.3954-0.46920.4839-0.2020.1508-0.06650.05020.3261-0.04210.1435-17.61786.3215-52.6201
23.5253-1.6388-1.00513.49582.57595.8278-0.10140.18730.0821-0.6576-0.14370.2758-0.2235-0.41420.24510.22670.0177-0.07580.1353-0.06220.1319-28.28153.8241-51.4747
31.1506-1.1536-1.71497.25682.55895.5562-0.0599-0.0738-0.42070.27560.21010.16250.80580.3471-0.15010.36020.0893-0.0980.3009-0.04190.3799-19.9985-9.4647-53.182
46.32562.8383-0.85986.34632.80465.82540.4263-0.3245-0.97570.3933-0.0903-0.11051.03-0.1092-0.3360.47490.0017-0.04740.17280.1440.4678-24.7902-3.2499-25.2501
55.86260.1240.94383.21071.69416.1058-0.0515-0.3867-0.31060.08-0.13370.38230.2932-0.63240.18530.0228-0.01860.0250.18210.00890.0802-29.05964.4868-26.1134
65.85631.9305-0.38825.6485-0.20756.95390.072-0.27130.5419-0.1428-0.0180.3194-0.33920.0769-0.0540.02730.00510.01050.1987-0.02070.0706-17.970312.0572-23.2641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 94
2X-RAY DIFFRACTION2A95 - 157
3X-RAY DIFFRACTION3A158 - 222
4X-RAY DIFFRACTION4B6 - 95
5X-RAY DIFFRACTION5B96 - 171
6X-RAY DIFFRACTION6B172 - 223

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