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- PDB-5yw1: Crystal structure of full length NS3 protein (eD4NS2BNS3) in comp... -

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Basic information

Entry
Database: PDB / ID: 5yw1
TitleCrystal structure of full length NS3 protein (eD4NS2BNS3) in complex with Bovine Pancreatic Trypsin Inhibitor
Components
  • FLAVIVIRUS_NS2B
  • PTI protein
  • Peptidase S7
KeywordsVIRAL PROTEIN / SERINE PROTEASE / NON-STRUCTURAL PROTEIN 3 / DEAH HELICASE / ATPASE / DENGUE VIRUS / FLAVIVIRUS
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 ...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 endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / 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 / 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 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 / 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
PTI protein / Genome polyprotein / Pancreatic trypsin inhibitor / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 4
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPhoo, W.W. / El Sahili, A.
Funding support Singapore, 4items
OrganizationGrant numberCountry
START UP GRANT Singapore
CBRG14MAY051 Singapore
CBRG/0103/2016 Singapore
National Research Foundation (Singapore)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. / Sahili, A.E. / Zhang, Z.Z. / Chen, M.W. / Lescar, J. / Vasudevan, S. / Luo, D.
History
DepositionNov 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Peptidase S7
A: FLAVIVIRUS_NS2B
I: PTI protein


Theoretical massNumber of molelcules
Total (without water)81,8203
Polymers81,8203
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-31 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.018, 87.493, 86.455
Angle α, β, γ (deg.)90.00, 98.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidase S7


Mass: 69517.266 Da / Num. of mol.: 1 / Fragment: UNP residues 1475-2092
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 FLAVIVIRUS_NS2B


Mass: 5930.479 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: W0LLP9
#3: Protein PTI protein / Pancreatic Trypsin Inhibitor


Mass: 6372.435 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) / Gene: PTI / Production host: Escherichia coli (E. coli) / References: UniProt: A6QPK7, UniProt: P00974*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES pH 6.0, 12% PEG4000 / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 24153 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 54.01 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.075 / Rrim(I) all: 0.112 / Net I/σ(I): 10.2
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3202 / CC1/2: 0.738 / Rpim(I) all: 0.727 / Rrim(I) all: 1.088 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VBC

2vbc


Resolution: 2.6→44.998 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 1175 4.87 %Randon Selection
Rwork0.2205 ---
obs0.2215 24103 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→44.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 0 2 5278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035395
X-RAY DIFFRACTIONf_angle_d0.6847327
X-RAY DIFFRACTIONf_dihedral_angle_d16.0743253
X-RAY DIFFRACTIONf_chiral_restr0.046808
X-RAY DIFFRACTIONf_plane_restr0.005959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71830.34961410.33292845X-RAY DIFFRACTION100
2.7183-2.86160.28981450.29662859X-RAY DIFFRACTION99
2.8616-3.04090.30861530.28132833X-RAY DIFFRACTION100
3.0409-3.27560.27211270.27522888X-RAY DIFFRACTION100
3.2756-3.60510.28671510.23492862X-RAY DIFFRACTION100
3.6051-4.12650.23871460.20772876X-RAY DIFFRACTION100
4.1265-5.19770.19791590.17892850X-RAY DIFFRACTION100
5.1977-45.00450.20651530.18882915X-RAY DIFFRACTION99
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)
11.93390.2839-0.59972.1043-1.9623.7134-0.03710.4578-0.11450.05770.2304-0.0952-0.4841-1.8408-0.14180.67240.00830.01691.19360.12570.527263.3057-1.0851.875
22.2973-0.77430.04781.25870.73790.97340.0888-0.2877-0.33850.1441-0.05990.04980.1011-0.1138-0.04520.3595-0.0478-0.01220.35760.05910.403352.40884.216317.1485
31.22260.05260.40932.3671.36812.16940.13140.041-0.2169-0.4524-0.26540.2761-0.1946-0.23290.09690.38240.0472-0.00450.30980.01580.375748.4081.0281-3.8818
40.0068-0.00260.01440.0618-0.06210.07960.32350.45690.29-0.25620.02450.1879-0.0464-0.2285-0.33320.9099-0.47690.06821.2179-0.10530.878864.2817-13.446942.8208
51.72561.51680.92844.2612-0.86651.4637-0.5885-0.158-0.21020.0573-0.31910.3390.3071-0.48510.3640.8568-0.4509-0.07331.61650.03030.903955.9377-11.124555.685
61.5630.0082-1.22390.11720.07981.0280.0066-0.0067-0.2192-0.1309-0.228-0.07160.54530.23760.16131.326-0.0694-0.01251.29750.10941.053655.2136-6.304667.9539
72.0938-0.2972-0.60812.1747-0.99523.06460.42450.0383-0.10750.08030.0947-0.089-0.1649-0.1988-0.18651.1645-0.12790.05071.1256-0.00220.649268.30473.896968.6725
85.0078-0.42640.17252.2504-0.70640.2919-0.0459-0.0898-0.2957-0.11810.0107-0.50090.10810.80640.00511.4475-0.05450.29550.85230.21050.608573.987112.451750.9158
90.7124-0.5019-1.10380.95310.65232.161-0.0826-0.16970.36760.4653-0.4492-0.1524-0.45561.0770.31580.8493-0.2404-0.06191.33490.52860.774986.5766-0.253247.0147
100.5305-0.1865-0.7051.00370.9281.4174-0.60360.4715-0.1165-0.2444-0.4989-0.57990.7820.4601-0.21440.7405-0.29530.35841.41150.45320.74489.2384-8.096944.1449
112.6940.7766-0.14471.2864-1.01571.9261-0.08240.3577-0.5167-0.7141-0.4104-0.6333-0.11490.60830.41370.7612-0.02020.20361.13630.27980.809585.2994-3.554840.965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 163 )
2X-RAY DIFFRACTION2chain 'B' and (resid 164 through 429 )
3X-RAY DIFFRACTION3chain 'B' and (resid 430 through 618 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 54 )
5X-RAY DIFFRACTION5chain 'A' and (resid 55 through 59 )
6X-RAY DIFFRACTION6chain 'A' and (resid 60 through 64 )
7X-RAY DIFFRACTION7chain 'A' and (resid 65 through 74 )
8X-RAY DIFFRACTION8chain 'A' and (resid 75 through 86 )
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 17 )
10X-RAY DIFFRACTION10chain 'I' and (resid 18 through 31 )
11X-RAY DIFFRACTION11chain 'I' and (resid 32 through 55 )

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