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- PDB-5o36: Japanese encephalitis virus non-structural protein 1' C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 5o36
TitleJapanese encephalitis virus non-structural protein 1' C-terminal domain
ComponentsJapanese encephalitis virus non-structural protein 1' (NS1'),Japanese encephalitis virus non-structural protein 1' (NS1')
KeywordsVIRAL PROTEIN / Flavivirus protein / NS1' / Japanese encephalitis
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell surface / 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 type I interferon-mediated signaling pathway / viral translational frameshifting / 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 / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
N-PROPANOL / Structural polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesJapanese encephalitis virus strain SA-14
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsThanalai, P. / Wright, G.S.A. / Antonyuk, S.V.
CitationJournal: J. Virol. / Year: 2018
Title: Structural Study of the C-Terminal Domain of Nonstructural Protein 1 from Japanese Encephalitis Virus.
Authors: Poonsiri, T. / Wright, G.S.A. / Diamond, M.S. / Turtle, L. / Solomon, T. / Antonyuk, S.V.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 28, 2018Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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
A: Japanese encephalitis virus non-structural protein 1' (NS1'),Japanese encephalitis virus non-structural protein 1' (NS1')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,22814
Polymers26,0151
Non-polymers1,21313
Water1,63991
1
A: Japanese encephalitis virus non-structural protein 1' (NS1'),Japanese encephalitis virus non-structural protein 1' (NS1')
hetero molecules

A: Japanese encephalitis virus non-structural protein 1' (NS1'),Japanese encephalitis virus non-structural protein 1' (NS1')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,45528
Polymers52,0302
Non-polymers2,42626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area6240 Å2
ΔGint-298 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.320, 77.940, 163.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Japanese encephalitis virus non-structural protein 1' (NS1'),Japanese encephalitis virus non-structural protein 1' (NS1')


Mass: 26014.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Japanese encephalitis virus strain SA-14
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27395, UniProt: P0DOH7*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.38 Å3/Da / Density % sol: 63.65 % / Description: needle
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.0 M Ammonium sulfate, 5% (v/v) propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→81.75 Å / Num. obs: 10247 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.141 / Net I/σ(I): 7.1
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.413 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1203 / CC1/2: 0.462 / Rpim(I) all: 1.03 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4oie

4oie


Resolution: 2.6→81.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.101 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22431 527 5.1 %RANDOM
Rwork0.16707 ---
obs0.16994 9719 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.397 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2--2.61 Å20 Å2
3----2.4 Å2
Refinement stepCycle: 1 / Resolution: 2.6→81.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 64 91 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191510
X-RAY DIFFRACTIONr_bond_other_d0.0020.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9662059
X-RAY DIFFRACTIONr_angle_other_deg1.02233060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4655177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19823.62369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84115241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3841511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211633
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02334
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1043.579711
X-RAY DIFFRACTIONr_mcbond_other3.0813.575710
X-RAY DIFFRACTIONr_mcangle_it4.8495.354887
X-RAY DIFFRACTIONr_mcangle_other4.8465.359888
X-RAY DIFFRACTIONr_scbond_it4.7534.29797
X-RAY DIFFRACTIONr_scbond_other4.7534.29797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1646.2451173
X-RAY DIFFRACTIONr_long_range_B_refined9.328.911641
X-RAY DIFFRACTIONr_long_range_B_other9.29728.931642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 45 -
Rwork0.247 684 -
obs--99.73 %

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