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- PDB-8r2l: Crystal structure of the ectodomain of TBEV E protein (Sofjin strain) -

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Basic information

Entry
Database: PDB / ID: 8r2l
TitleCrystal structure of the ectodomain of TBEV E protein (Sofjin strain)
ComponentsEnvelope protein E
KeywordsVIRAL PROTEIN / envelope protein E / tick-borne enciphalitis
Function / homology
Function and homology information


flavivirin / 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 / methyltransferase cap1 activity ...flavivirin / 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 / 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 innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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
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. ...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
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsVlaskina, A.V. / Samygina, V.R.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation Russian Federation
CitationJournal: Crystals / Year: 2023
Title: Self-Assembly and Conformational Change in the Oligomeric Structure of the Ectodomain of the TBEV E Protein Studied via X-ray, Small-Angle X-ray Scattering, and Molecular Dynamics
Authors: Konarev, P.V. / Vlaskina, A.V. / Korzhenevskiy, D. / Rakitina, T.V. / Petrenko, D. / Agapova, Y. / Kordonskaya, Y. / Samygina, V.R.
History
DepositionNov 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Envelope protein E


Theoretical massNumber of molelcules
Total (without water)43,3871
Polymers43,3871
Non-polymers00
Water1448
1
AAA: Envelope protein E

AAA: Envelope protein E


Theoretical massNumber of molelcules
Total (without water)86,7752
Polymers86,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
Buried area3460 Å2
ΔGint-16 kcal/mol
Surface area37200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.061, 165.061, 165.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Envelope protein E


Mass: 43387.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus (STRAIN SOFJIN)
Production host: Escherichia coli (E. coli) / References: UniProt: P07720
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: Ammonium sulfate, MPD, citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.89999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89999 Å / Relative weight: 1
ReflectionResolution: 3.2→116.4 Å / Num. obs: 50365 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.94 / Net I/σ(I): 32.5
Reflection shellResolution: 3.2→3.42 Å / Num. unique obs: 878 / Rpim(I) all: 0.221

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.906 / SU B: 22.923 / SU ML: 0.366 / Cross valid method: FREE R-VALUE / ESU R: 2.232 / ESU R Free: 0.463
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2865 650 4.977 %
Rwork0.202 12410 -
all0.206 --
obs-13060 98.7 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 110.944 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 0 8 3036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133102
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172838
X-RAY DIFFRACTIONr_angle_refined_deg2.4611.6444216
X-RAY DIFFRACTIONr_angle_other_deg1.3791.5786602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.4335393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67722.778144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.4515521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9731515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023463
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02618
X-RAY DIFFRACTIONr_nbd_refined0.2580.2694
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2320.22924
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21333
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.21645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.215
X-RAY DIFFRACTIONr_nbd_other0.230.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.22
X-RAY DIFFRACTIONr_mcbond_it15.14311.6661575
X-RAY DIFFRACTIONr_mcbond_other15.14411.6681574
X-RAY DIFFRACTIONr_mcangle_it21.40917.4911967
X-RAY DIFFRACTIONr_mcangle_other21.40617.4911968
X-RAY DIFFRACTIONr_scbond_it16.40812.3551526
X-RAY DIFFRACTIONr_scbond_other16.40312.3571527
X-RAY DIFFRACTIONr_scangle_it22.88418.132249
X-RAY DIFFRACTIONr_scangle_other22.87918.1332250
X-RAY DIFFRACTIONr_lrange_it27.528135.0123245
X-RAY DIFFRACTIONr_lrange_other27.524135.0463246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.362380.323864X-RAY DIFFRACTION100
3.28-3.3650.342380.31846X-RAY DIFFRACTION100
3.365-3.4570.51510.308819X-RAY DIFFRACTION100
3.457-3.5580.357360.274805X-RAY DIFFRACTION100
3.558-3.6680.401520.266768X-RAY DIFFRACTION100
3.668-3.7880.335490.251746X-RAY DIFFRACTION100
3.788-3.9220.355480.258722X-RAY DIFFRACTION100
3.922-4.070.408320.241716X-RAY DIFFRACTION100
4.07-4.2370.275320.198690X-RAY DIFFRACTION100
4.237-4.4260.194320.162658X-RAY DIFFRACTION100
4.426-4.6430.171300.146640X-RAY DIFFRACTION100
4.643-4.8960.224340.149606X-RAY DIFFRACTION100
4.896-5.1950.193270.15584X-RAY DIFFRACTION100
5.195-5.5560.133260.185535X-RAY DIFFRACTION100
5.556-6.0040.413280.197508X-RAY DIFFRACTION100
6.004-6.5820.297230.198479X-RAY DIFFRACTION100
6.582-7.3680.364220.196430X-RAY DIFFRACTION100
7.368-8.5240.239170.182387X-RAY DIFFRACTION100
8-100.267220.181334X-RAY DIFFRACTION100
10.481-150.293130.202273X-RAY DIFFRACTION100

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