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- PDB-5yvu: Crystal structures of unlinked full length NS3 from Dengue virus ... -

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Basic information

Entry
Database: PDB / ID: 5yvu
TitleCrystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain
Components
  • (Genome polyprotein) x 2
  • Pancreatic trypsin inhibitor
KeywordsVIRAL PROTEIN / SERINE PROTEASE / NON-STRUCTURAL PROTEIN 3 / DEAH HELICASE / FLAVIVIRUS / DENGUE
Function / homology
Function and homology information


trypsinogen activation / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion ...trypsinogen activation / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / serine protease inhibitor complex / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / serine-type endopeptidase inhibitor activity / viral capsid / double-stranded RNA binding / channel activity / protease binding / monoatomic ion transmembrane transport / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / 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 / lipid binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular space / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / 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 ...: / Pancreatic trypsin inhibitor Kunitz domain / 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 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, 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 / P-loop containing nucleotide triphosphate hydrolases / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesDengue virus 4
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.491 Å
AuthorsPhoo, W.W. / El Sahili, A.
Funding support Singapore, 4items
OrganizationGrant numberCountry
NTUSTARTUP_GRANT Singapore
NMRCCBRG14051 Singapore
NMRCCBRG/0103/2016 Singapore
NRFNRF-CRP001-063 Singapore
CitationJournal: To Be Published
Title: Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain
Authors: Phoo, W.W. / El Sahili, A. / ZHANG, Z.Z. / CHEN, M.W. / VASUDEVAN, S. / LESCAR, J. / LUO, D.
History
DepositionNov 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Genome polyprotein
A: Genome polyprotein
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4444
Polymers82,3523
Non-polymers921
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-31 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.059, 85.627, 85.508
Angle α, β, γ (deg.)90.00, 97.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Genome polyprotein


Mass: 70044.766 Da / Num. of mol.: 1 / Fragment: UNP residues 1475-2092 / Mutation: S135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEL4
#2: Protein Genome polyprotein


Mass: 5964.470 Da / Num. of mol.: 1 / Fragment: UNP residues 1393-1439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEL4
#3: Protein Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPTI


Mass: 6342.387 Da / Num. of mol.: 1 / Fragment: UNP residues 36-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00974
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES pH 6.4, 12% PEG6000 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.491→47.7 Å / Num. obs: 50500 / % possible obs: 94.85 % / Redundancy: 3.4 % / Biso Wilson estimate: 52.42 Å2 / CC1/2: 0.917 / Rmerge(I) obs: 0.1176 / Rrim(I) all: 0.1389 / Net I/σ(I): 14.03
Reflection shellResolution: 2.491→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5446 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 2458 / CC1/2: 0.799 / Rrim(I) all: 0.1389 / % possible all: 92.82

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VBC

2vbc


Resolution: 2.491→47.704 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 30.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 2310 5 %Random selection
Rwork0.2219 ---
obs0.2241 46160 88.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.491→47.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 6 48 5350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025420
X-RAY DIFFRACTIONf_angle_d0.6467349
X-RAY DIFFRACTIONf_dihedral_angle_d12.6021979
X-RAY DIFFRACTIONf_chiral_restr0.025810
X-RAY DIFFRACTIONf_plane_restr0.004960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4914-2.54560.30451320.29962500X-RAY DIFFRACTION81
2.5456-2.60480.3231470.30532765X-RAY DIFFRACTION91
2.6048-2.670.38891390.34382669X-RAY DIFFRACTION85
2.67-2.74210.34871470.32052805X-RAY DIFFRACTION91
2.7421-2.82280.32171530.27892976X-RAY DIFFRACTION96
2.8228-2.91390.32631580.27932983X-RAY DIFFRACTION96
2.9139-3.01810.31251550.26872953X-RAY DIFFRACTION96
3.0181-3.13890.31311550.26592976X-RAY DIFFRACTION95
3.1389-3.28170.32391530.26012870X-RAY DIFFRACTION94
3.2817-3.45470.33871360.26292505X-RAY DIFFRACTION81
3.4547-3.6710.29791330.23622480X-RAY DIFFRACTION80
3.671-3.95440.22721310.21282445X-RAY DIFFRACTION79
3.9544-4.35210.22641490.18542876X-RAY DIFFRACTION92
4.3521-4.98120.21261480.16872755X-RAY DIFFRACTION89
4.9812-6.27360.24331420.19982673X-RAY DIFFRACTION87
6.2736-47.71280.20821320.16882619X-RAY DIFFRACTION84
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)
14.3841-0.4101-0.9342.6404-0.44098.9635-0.08370.5966-0.1585-0.0444-0.00540.4686-0.7701-2.46210.13340.64250.0547-0.04171.42750.12940.56910.7911-0.85951.6511
24.389-0.5196-0.19031.44480.29291.40630.0167-0.6798-0.31060.26140.03550.06410.2335-0.1953-0.04480.3393-0.1015-0.02520.44380.05720.3578-1.1144.207917.2575
33.77320.20012.44141.87111.65853.80270.098-0.08260.0894-0.2597-0.19270.1902-0.1475-0.35520.08410.3016-0.00510.04340.29970.06780.3325-3.05580.9728-2.5811
46.010.8177-4.05351.83080.49854.0501-0.42920.6099-0.04610.1193-0.49360.16280.4278-1.20580.84850.7599-0.3912-0.09971.55240.11550.70857.2873-7.626560.1391
56.3402-3.07041.51272.0011-1.46966.0559-0.4707-0.20430.7201-2.07380.0446-0.7599-0.4090.30680.36551.64530.13230.24010.78770.05740.778619.174211.327365.2152
65.43783.77234.3624.87933.84418.8959-0.82170.84390.3779-0.43740.0718-0.9128-3.79741.59190.70342.1757-0.2837-0.00411.07160.16650.924420.993813.969750.4411
76.689-1.3187-3.04522.2976-2.91137.4190.14130.61270.3677-0.2026-1.098-1.4858-1.92441.33450.91131.4139-0.20040.02441.52710.66960.799722.381710.940749.3855
86.35770.8491-3.44980.095-0.45391.8720.1156-0.45650.4941-0.009-0.5408-0.4039-0.45911.91960.48730.7738-0.2871-0.16042.24360.4730.761440.26290.595344.0673
92.0332-1.0163-1.92863.0159-0.4180.4391-0.44260.3922-0.2428-0.4352-0.5745-1.16460.51561.1221.00560.6979-0.22380.30721.45150.30410.956631.9551-6.256546.75
109.5478-2.5115-0.5555.82881.64082.2909-0.57060.1356-1.2922-1.1721-0.7296-2.14681.23111.23411.23050.4004-0.08120.16661.6140.78261.562432.1318-8.087145.9887
118.4318-3.76870.2656.7758-0.59856.98170.12841.27250.33880.6835-0.07480.1915-0.92370.6465-0.09870.6452-0.2315-0.0211.3810.4560.663330.3551-0.377642.4642
124.601-2.97-2.98122.53781.55222.15680.34310.1458-0.83221.1566-1.168-0.0063-1.64380.24680.76061.69130.28480.38421.67830.45660.943838.2532-7.822634.8693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 163 )
2X-RAY DIFFRACTION2chain 'B' and (resid 164 through 412 )
3X-RAY DIFFRACTION3chain 'B' and (resid 413 through 618 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 74 )
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 79 )
7X-RAY DIFFRACTION7chain 'A' and (resid 80 through 87 )
8X-RAY DIFFRACTION8chain 'I' and (resid 1 through 10 )
9X-RAY DIFFRACTION9chain 'I' and (resid 11 through 29 )
10X-RAY DIFFRACTION10chain 'I' and (resid 30 through 35 )
11X-RAY DIFFRACTION11chain 'I' and (resid 36 through 47 )
12X-RAY DIFFRACTION12chain 'I' and (resid 48 through 55 )

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