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- PDB-5yvj: Crystal structure of full length NS2B47-NS3 (gD4NS2BNS3) from Den... -

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Basic information

Entry
Database: PDB / ID: 5yvj
TitleCrystal structure of full length NS2B47-NS3 (gD4NS2BNS3) from Dengue virus 4 in open conformation
Components(Genome polyprotein) x 2
KeywordsVIRAL PROTEIN / Serine Protease / Helicase / Non-structural protein 3 / Dengue / Flavivirus
Function / homology
Function and homology information


: / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport ...: / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / 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 / lipid binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
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 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 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.508 Å
AuthorsPhoo, W.W. / El Sahili, A.
Funding support Singapore, 2items
OrganizationGrant numberCountry
NTUSTART UP GRANT Singapore
NMRCCBRG14May05 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. / Vasudevan, S. / Lescar, J. / Luo, D.
History
DepositionNov 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Genome polyprotein
C: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7953
Polymers74,7032
Non-polymers921
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Single monomeric peak in SEC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-14 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.780, 86.810, 75.900
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Genome polyprotein


Mass: 69501.266 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/peptide Genome polyprotein


Mass: 5201.639 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: Q2YHE8
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES pH7.5, 15% PEG 6000 / PH range: 7.5

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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: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.508→45.051 Å / Num. obs: 22654 / % possible obs: 96.26 % / Redundancy: 2.4 % / Biso Wilson estimate: 40.99 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.117 / Net I/σ(I): 5.52
Reflection shellResolution: 2.508→2.64 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2117 / CC1/2: 0.817 / Rpim(I) all: 0.299 / Rrim(I) all: 0.497 / % possible all: 90.87

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Processing

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

2vbc


Resolution: 2.508→45.051 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1137 5.02 %Random selection
Rwork0.1879 ---
obs0.1907 22644 96.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.508→45.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 6 124 4843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054824
X-RAY DIFFRACTIONf_angle_d0.8466536
X-RAY DIFFRACTIONf_dihedral_angle_d12.861797
X-RAY DIFFRACTIONf_chiral_restr0.032716
X-RAY DIFFRACTIONf_plane_restr0.004848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5081-2.62220.36961510.2652537X-RAY DIFFRACTION92
2.6222-2.76050.30171390.23852626X-RAY DIFFRACTION96
2.7605-2.93340.28581380.22782666X-RAY DIFFRACTION95
2.9334-3.15980.28231430.22312724X-RAY DIFFRACTION98
3.1598-3.47770.27271610.20012721X-RAY DIFFRACTION98
3.4777-3.98070.22771230.17762729X-RAY DIFFRACTION97
3.9807-5.01420.20191470.15142735X-RAY DIFFRACTION97
5.0142-45.05860.21171350.16772769X-RAY DIFFRACTION97
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)
14.44441.4701-0.17934.10521.29876.6663-0.09550.35560.3491-0.56650.25030.0282-0.44420.2687-0.13520.62460.04920.02790.4983-0.00480.361530.710447.628.8068
21.22030.61132.26190.48551.34413.8495-0.5467-0.23340.7069-0.604-0.20890.4022-0.5172-0.52380.66910.51410.0217-0.08880.450.01520.440642.395459.741645.4309
33.7706-0.0576-0.16493.4386-0.71273.2869-0.06510.3372-0.0247-0.315-0.0849-0.13860.04320.13310.13780.236-0.01340.03020.257800.217159.059252.034858.8595
41.97580.26891.12540.9836-0.44232.06880.0802-0.1487-0.16650.1351-0.00920.00930.07640.0038-0.09630.26350.03120.05870.23880.00160.269746.879440.468274.6062
58.5535-4.88335.97237.8988-4.40469.2751-0.5246-0.57220.0526-0.45550.37260.33620.3042-0.22830.15640.7056-0.02360.03570.5207-0.02720.388236.804547.234522.5132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 18 through 150 )
2X-RAY DIFFRACTION2chain 'B' and (resid 151 through 191 )
3X-RAY DIFFRACTION3chain 'B' and (resid 192 through 324 )
4X-RAY DIFFRACTION4chain 'B' and (resid 325 through 618 )
5X-RAY DIFFRACTION5chain 'C' and (resid 49 through 63 )

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