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- PDB-2fp7: West Nile Virus NS2B/NS3protease in complex with Bz-Nle-Lys-Arg-Arg-H -

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Basic information

Entry
Database: PDB / ID: 2fp7
TitleWest Nile Virus NS2B/NS3protease in complex with Bz-Nle-Lys-Arg-Arg-H
Components
  • (Genome polyprotein) x 2
  • N-benzoyl-L-norleucyl-L-lysyl-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-argininamide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Flavivirus / NS3 protease / NS2B cofactor / substrate-based inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity ...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 JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / positive regulation of viral genome replication / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein-DNA complex / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Thrombin, subunit H - #120 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / 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 / Trypsin-like serine proteases / 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
N-benzoyl-L-norleucyl-6-ammonio-L-norleucyl-N~5~-[amino(iminio)methyl]-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-ornithinamide / Genome polyprotein
Similarity search - Component
Biological speciesWest Nile virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSchiering, N. / D'Arcy, A. / Erbel, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus.
Authors: Erbel, P. / Schiering, N. / D'Arcy, A. / Renatus, M. / Kroemer, M. / Lim, S.P. / Yin, Z. / Keller, T.H. / Vasudevan, S.G. / Hommel, U.
History
DepositionJan 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 2, 2011Group: Structure summary
Revision 1.4Feb 27, 2013Group: Other
Revision 1.5Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_ref_seq_dif.details
Revision 1.6Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.7Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: N-benzoyl-L-norleucyl-L-lysyl-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-argininamide


Theoretical massNumber of molelcules
Total (without water)25,3543
Polymers25,3543
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-33 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.425, 93.425, 47.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is a monomer

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Components

#1: Protein Genome polyprotein


Mass: 6101.576 Da / Num. of mol.: 1 / Fragment: NS2b
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P06935, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Protein Genome polyprotein


Mass: 18588.094 Da / Num. of mol.: 1 / Fragment: NS3pro
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P06935, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#3: Protein/peptide N-benzoyl-L-norleucyl-L-lysyl-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-argininamide


Type: Peptide-like / Class: Inhibitor / Mass: 663.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: N-benzoyl-L-norleucyl-6-ammonio-L-norleucyl-N~5~-[amino(iminio)methyl]-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-ornithinamide
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 2 M ammonioum sulfate, 100mM HEPES., pH 8.5, VAPOR DIFFUSION, temperature 321K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 1.68→81 Å / Num. all: 26547 / Num. obs: 26547 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 21.5
Reflection shellResolution: 1.68→1.73 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.313 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse - obtained by SAD phasing

Resolution: 1.68→46.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.533 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1328 5 %RANDOM
Rwork0.18054 ---
obs0.18247 25216 97.87 %-
all-25216 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å2-0.66 Å20 Å2
2---1.32 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 1.68→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 0 133 1619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221523
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9692060
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.99624.84866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16715241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.465157
X-RAY DIFFRACTIONr_chiral_restr0.1050.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021161
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.2619
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21026
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9131.5944
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48521479
X-RAY DIFFRACTIONr_scbond_it2.0343675
X-RAY DIFFRACTIONr_scangle_it3.1384.5580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 93 -
Rwork0.236 1762 -
obs--92.11 %
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)
14.6974-1.94510.30633.2111-0.73131.1726-0.041-0.0386-0.4780.03170.11270.42010.0284-0.0376-0.0716-0.1169-0.00290.0601-0.1214-0.0108-0.071227.970651.09381.4177
23.5625-1.56220.05412.5352-0.17740.8569-0.0847-0.2318-0.3470.15980.08470.1868-0.01080.00880-0.07340.0080.0462-0.07120.0052-0.034830.613950.94064.7447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA49 - 886 - 45
2X-RAY DIFFRACTION2BB19 - 274 - 12
3X-RAY DIFFRACTION2BB33 - 16818 - 153

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