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- PDB-3e90: West Nile vi rus NS2B-NS3protease in complexed with inhibitor Nap... -

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Basic information

Entry
Database: PDB / ID: 3.0E+90
TitleWest Nile vi rus NS2B-NS3protease in complexed with inhibitor Naph-KKR-H
Components
  • NS2B cofactor
  • NS3 protease
KeywordsHYDROLASE / West Nile virus / NS3 protease / trypsin-like serine protease / protease inhibitor / catalytic histidine / induced fit / ATP-binding / Capsid protein / Helicase / Nucleotide-binding / RNA replication / Transmembrane / Virion
Function / homology
Function and homology information


RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / symbiont-mediated suppression of host apoptosis / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / positive regulation of viral genome replication ...RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / symbiont-mediated suppression of host apoptosis / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / positive regulation of viral genome replication / 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 / protein-DNA complex / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / peptidase activity / 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 / ribonucleoprotein complex / 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 / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / 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 ...Thrombin, subunit H - #120 / 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 / Trypsin-like serine proteases / 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
Chem-NKK / Genome polyprotein
Similarity search - Component
Biological speciesWest Nile virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMartin, J.L. / Robin, G.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of West Nile virus NS3 protease: ligand stabilization of the catalytic conformation
Authors: Robin, G. / Chappell, K. / Stoermer, M.J. / Hu, S.-H. / Young, P.R. / Fairlie, D.P. / Martin, J.L.
History
DepositionAug 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS2B cofactor
B: NS3 protease
C: NS2B cofactor
D: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6336
Polymers53,4964
Non-polymers1,1372
Water3,639202
1
A: NS2B cofactor
B: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3173
Polymers26,7482
Non-polymers5691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-25 kcal/mol
Surface area11230 Å2
MethodPISA
2
C: NS2B cofactor
D: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3173
Polymers26,7482
Non-polymers5691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-31 kcal/mol
Surface area10320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-60 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.511, 165.915, 79.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailseach biological unit consists of cofactor(A or C) and protease(C or D)

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Components

#1: Protein/peptide NS2B cofactor


Mass: 5378.704 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Strain: WNV NY99-4132 / Gene: NS2B-NS3PROTEASE / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P06935*PLUS
#2: Protein NS3 protease


Mass: 21369.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Strain: WNV NY99-4132 / Gene: NS2B-NS3PROTEASE / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P06935*PLUS, flavivirin
#3: Chemical ChemComp-NKK / N~2~-(naphthalen-2-ylcarbonyl)-L-lysyl-N-[(1S)-4-carbamimidamido-1-formylbutyl]-L-lysinamide


Mass: 568.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H44N8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHIS LIGAND CAN BE CALLED AS 2-NAPHTHOYL-LYS-LYS-ARG-H.
Sequence detailsTHIS SEQUENCE HAS BEEN DEPOSITED ON GB WITH ACCESSION CODE, FM867597. IT WILL SHOW UP IN UNIPROT ...THIS SEQUENCE HAS BEEN DEPOSITED ON GB WITH ACCESSION CODE, FM867597. IT WILL SHOW UP IN UNIPROT LATER. THE FIRST TWO RESIDUES MG AND LAST FOUR RESIDUES GGGG IN CHAINS A & C ARE EXPRESSION TAGS AND LINKER, RESPECTIVELY. IN CHAINS B & D, THE FIRST FOUR RESIDUES SGGG ARE LINKER. THE LAST FOUR RESIDUES GSRS AND FOLLOWING SIX RESIDUES HHHHHH ARE LINKER AND EXPRESSION TAGS, RESPECTIVELY.

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 3.5M sodium formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2007 / Details: Osmic Confocal Max-Flux (HiRes2)
RadiationMonochromator: Osmic confocal Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 53250 / Num. obs: 20604 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 7
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2042 / % possible all: 94.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FP7

2fp7


Resolution: 2.45→36.81 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 917 4.2 %Random
Rwork0.197 ---
all-19212 --
obs-19212 88.2 %-
Solvent computationBsol: 44.634 Å2
Displacement parametersBiso max: 70.17 Å2 / Biso min: 2.62 Å2
Baniso -1Baniso -2Baniso -3
1--6.318 Å20 Å20 Å2
2--2.891 Å20 Å2
3---3.427 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.45→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 82 202 3594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.706
X-RAY DIFFRACTIONc_mcbond_it1.3191.5
X-RAY DIFFRACTIONc_scbond_it1.8742
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scangle_it2.7662.5
LS refinement shellResolution: 2.45→2.54 Å
RfactorNum. reflection
Rfree0.324 80
Rwork0.273 -
obs-1671
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3inhib-C-24-par+patch.param

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