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- PDB-2ijo: Crystal Structure of the West Nile virus NS2B-NS3 protease comple... -

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Basic information

Entry
Database: PDB / ID: 2ijo
TitleCrystal Structure of the West Nile virus NS2B-NS3 protease complexed with bovine pancreatic trypsin inhibitor
Components
  • (Polyprotein) x 2
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / WEST NILE VIRUS / PROTEASE / APROTININ / BPTI / NS2B / NS3 / FLAVIVIRUS / serine protease / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / DNA/DNA annealing activity / RNA folding chaperone / RNA strand annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / trypsinogen activation / symbiont-mediated suppression of host apoptosis / negative regulation of serine-type endopeptidase activity / sulfate binding ...RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / DNA/DNA annealing activity / RNA folding chaperone / RNA strand annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / trypsinogen activation / symbiont-mediated suppression of host apoptosis / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / 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 / serine protease inhibitor complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / serine-type endopeptidase inhibitor activity / protein-DNA complex / viral capsid / peptidase activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protease binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / 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 innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / ribonucleoprotein complex / 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 / viral envelope / calcium ion binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / DNA binding / extracellular space / RNA binding / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Thrombin, subunit H - #120 / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. ...: / Pancreatic trypsin inhibitor Kunitz domain / Thrombin, subunit H - #120 / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / 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 / Few Secondary Structures / Irregular / 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
Pancreatic trypsin inhibitor / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesWest Nile virus
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAleshin, A.E. / Shiryaev, S.A. / Strongin, A.Y. / Liddington, R.C.
CitationJournal: Protein Sci. / Year: 2007
Title: Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold.
Authors: Aleshin, A.E. / Shiryaev, S.A. / Strongin, A.Y. / Liddington, R.C.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 400 COMPOUND THE PROTEINS NS2B (CHAIN A) AND NS3 (CHAIN B) ARE CONNECTED THROUGH A LINKER AGGGGSGGGG.
Remark 999 SEQUENCE THIS IS THE SEQUENCE OF THE LINKER BETWEEN CHAINS A AND B. RESIDUE NUMBERS 1 THROUGH 5 IN ... SEQUENCE THIS IS THE SEQUENCE OF THE LINKER BETWEEN CHAINS A AND B. RESIDUE NUMBERS 1 THROUGH 5 IN COORDINATES FOR CHAIN B ARE ARBITRARY, SINCE ONLY THESE FIVE RESIDUES WERE VISIBLE IN ELECTRON DENSITY. THE SEQUENCE ALIGNMENT OF THESE FIVE RESIDUES IS ALSO ARBITRARY AND IS BASED ONLY ON THE DISTANCE CRITERIA TO THE NEXT VISIBLE RESIDUES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyprotein
B: Polyprotein
I: Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)33,5133
Polymers33,5133
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-33 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.050, 72.177, 79.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsNS2B cofactor and NS3 protease domain form heterodimer

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Components

#1: Protein Polyprotein / NON-STRUCTURAL PROTEIN 2B / NS2B


Mass: 6078.417 Da / Num. of mol.: 1 / Fragment: NS2B cofactor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: pET101 / Production host: Escherichia coli (E. coli)
References: UniProt: Q203W3, UniProt: P06935*PLUS, flavivirin
#2: Protein Polyprotein / NON-STRUCTURAL PROTEIN 3 / NS3


Mass: 20906.584 Da / Num. of mol.: 1 / Fragment: NS3 protease domain / Mutation: K104R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: pET101 / Production host: Escherichia coli (E. coli)
References: UniProt: Q203W3, UniProt: P06935*PLUS, flavivirin
#3: Protein Pancreatic trypsin inhibitor / Basic protease inhibitor / BPI / BPTI / Aprotinin


Mass: 6527.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00974
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 8000, 0.1M TRIS-HCL, 0.2M SODIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 11411 / Num. obs: 11411 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24
Reflection shellResolution: 2.3→2.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 / % possible all: 70

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GGV

2ggv


Resolution: 2.3→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 544 4.4 %random
Rwork0.212 ---
obs0.212 11411 93 %-
all-11411 --
Solvent computationBsol: 42.735 Å2
Displacement parametersBiso mean: 44.735 Å2
Baniso -1Baniso -2Baniso -3
1-2.797 Å20 Å20 Å2
2---6.386 Å20 Å2
3---3.589 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 0 89 2112
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.456
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_scbond_it2.3312
X-RAY DIFFRACTIONc_mcangle_it2.7672
X-RAY DIFFRACTIONc_scangle_it3.5182.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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