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- PDB-5mv2: Crystal structure of the E protein of the Japanese encephalitis l... -

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Basic information

Entry
Database: PDB / ID: 5mv2
TitleCrystal structure of the E protein of the Japanese encephalitis live attenuated vaccine virus
ComponentsE protein
KeywordsVIRAL PROTEIN / viral envelope glycoprotein
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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell ...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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / 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 / symbiont entry into host cell / 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
Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus ...Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / 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 / 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 / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesJapanese encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, X. / Zhao, X. / Na, R. / Li, L. / Warkentin, E. / Witt, J. / Lu, X. / Wei, Y. / Peng, G. / Li, Y. / Wang, J.
CitationJournal: Protein Cell / Year: 2019
Title: The structure differences of Japanese encephalitis virus SA14 and SA14-14-2 E proteins elucidate the virulence attenuation mechanism.
Authors: Liu, X. / Zhao, X. / Na, R. / Li, L. / Warkentin, E. / Witt, J. / Lu, X. / Yu, Y. / Wei, Y. / Peng, G. / Li, Y. / Wang, J.
History
DepositionJan 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: 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 1.3Nov 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
A: E protein


Theoretical massNumber of molelcules
Total (without water)44,8271
Polymers44,8271
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.600, 55.900, 90.100
Angle α, β, γ (deg.)90.00, 132.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E protein


Mass: 44826.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Japanese encephalitis virus (strain SA-14)
Strain: SA-14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8QQT1, UniProt: P27395*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 0.2M Tri-Na citrate, pH 7.9, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97621 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97621 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28195 / % possible obs: 98.7 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.877 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mv1

5mv1


Resolution: 2.1→19.944 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 1409 5 %
Rwork0.1802 --
obs0.1824 28165 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 0 236 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123177
X-RAY DIFFRACTIONf_angle_d1.1854310
X-RAY DIFFRACTIONf_dihedral_angle_d14.4011876
X-RAY DIFFRACTIONf_chiral_restr0.073479
X-RAY DIFFRACTIONf_plane_restr0.008555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1750.33091390.27522637X-RAY DIFFRACTION99
2.175-2.26190.30031410.25262674X-RAY DIFFRACTION99
2.2619-2.36470.31061390.2462646X-RAY DIFFRACTION99
2.3647-2.48920.33841390.25612642X-RAY DIFFRACTION99
2.4892-2.64480.28171400.22942664X-RAY DIFFRACTION99
2.6448-2.84850.27361410.20582676X-RAY DIFFRACTION99
2.8485-3.13420.23481410.17582673X-RAY DIFFRACTION100
3.1342-3.58540.17351410.15862687X-RAY DIFFRACTION100
3.5854-4.50860.18971430.1452710X-RAY DIFFRACTION100
4.5086-19.94510.18581450.15742747X-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)
12.9895-0.20451.30220.0727-0.00370.6806-0.0165-0.2453-0.02580.0470.0095-0.0081-0.0049-0.0447-0.03810.3673-0.0032-0.04080.37560.02930.330917.0745-9.290240.0781
26.40430.60211.43490.39340.16510.94910.0352-0.4667-0.22590.0917-0.0357-0.00110.0756-0.0348-0.04140.3808-0.01390.02310.33190.02360.289919.2138-12.406643.5263
31.6053-0.44161.04750.1241-0.22292.3884-0.0685-0.2794-0.1895-0.01750.1690.2052-0.1931-0.4363-0.05030.3613-0.0233-0.0470.39330.00980.4756-8.5943-11.454127.5494
43.22690.45521.23712.0553-0.77595.2105-0.06010.3008-0.4135-0.15580.0950.24010.1421-0.5165-0.08760.3409-0.0008-0.11250.3548-0.07540.3943-19.2773-13.43758.2609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 163 )
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 265 )
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 312 )
4X-RAY DIFFRACTION4chain 'A' and (resid 313 through 400 )

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