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- PDB-8r8l: The structure of inactivated mature tick-borne encephalitis virus -

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Basic information

Entry
Database: PDB / ID: 8r8l
TitleThe structure of inactivated mature tick-borne encephalitis virus
ComponentsPeptide 2k
KeywordsVIRUS / TBEV / cryo-EM / Tick-Borne Encephalitis Virus
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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase 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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C ...: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsPichkur, E.B. / Samygina, V.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Emerg Microbes Infect / Year: 2024
Title: The structure of inactivated mature tick-borne encephalitis virus at 3.0 Å resolution.
Authors: Evgeny B Pichkur / Mikhail F Vorovitch / Alla L Ivanova / Elena V Protopopova / Valery B Loktev / Dmitry I Osolodkin / Aydar A Ishmukhametov / Valeriya R Samygina /
Abstract: Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE ...Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE cases are registered annually despite the availability of effective formaldehyde-inactivated full-virion vaccines due to insufficient vaccination coverage, as well as sporadic cases of vaccine breakthrough. The development of improved vaccines would benefit from the atomic resolution structure of the antigen. Here we report the refined single-particle cryo-electron microscopy (cryo-EM) structure of the inactivated mature TBEV vaccine strain Sofjin-Chumakov (Far-Eastern subtype) at a resolution of 3.0 Å. The increase of the resolution with respect to the previously published structures of TBEV strains Hypr and Kuutsalo-14 (European subtype) was reached due to improvement of the virus sample quality achieved by the optimized preparation methods. All the surface epitopes of TBEV were structurally conserved in the inactivated virions. ELISA studies with monoclonal antibodies supported the hypothesis of TBEV protein shell cross-linking upon inactivation with formaldehyde.
History
DepositionNov 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Structure summary / Category: audit_author / em_author_list / Item: _audit_author.name / _em_author_list.author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide 2k
B: Peptide 2k
C: Peptide 2k
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7926
Polymers130,1293
Non-polymers6643
Water0
1
A: Peptide 2k
B: Peptide 2k
C: Peptide 2k
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,847,540360
Polymers7,807,723180
Non-polymers39,817180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.80901699, -0.5, 0.30901699), (-0.5, 0.30901699, -0.80901699), (0.30901699, -0.80901699, -0.5)690.39990817, 690.39994812, 690.39997281
3given(1), (-1), (-1)-3.052E-5, 690.39996338, 690.39993286
4given(0.80901699, -0.5, -0.30901699), (-0.5, -0.30901699, -0.80901699), (0.30901699, 0.80901699, -0.5)345.19997586, 903.74526972, 131.85466952
5given(0.5, 0.30901699, -0.80901699), (-0.30901699, -0.80901699, -0.5), (-0.80901699, 0.5, -0.30901699)345.19996643, 903.74527555, 558.5452786
6given(-0.30901699, -0.80901699, -0.5), (-0.80901699, 0.5, -0.30901699), (0.5, 0.30901699, -0.80901699)903.74524503, 558.5452786, 345.19999695
7given(-0.80901699, 0.5, -0.30901699), (0.5, 0.30901699, -0.80901699), (-0.30901699, -0.80901699, -0.5)558.54524808, 345.19999695, 903.74527555
8given(-0.80901699, -0.5, -0.30901699), (0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5)903.74522977, 558.54531855, 345.19999112
9given(-0.30901699, 0.80901699, -0.5), (-0.80901699, -0.5, -0.30901699), (-0.5, 0.30901699, 0.80901699)345.19994174, 903.74526029, 131.85464483
10given(0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699)558.54528803, 345.19997226, -213.34529691
11given(-1), (-1), (1)690.39993286, 690.39993286
12given(-0.5, -0.30901699, -0.80901699), (0.30901699, 0.80901699, -0.5), (0.80901699, -0.5, -0.30901699)903.7452392, 131.85466952, 345.20000638
13given(-0.5, 0.30901699, -0.80901699), (0.30901699, -0.80901699, -0.5), (-0.80901699, -0.5, 0.30901699)690.3999176, 690.39997281, 690.39993869
14given(-0.30901699, -0.80901699, -0.5), (0.80901699, -0.5, 0.30901699), (-0.5, -0.30901699, 0.80901699)903.74524503, 131.85468478, 345.19996643
15given(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)558.54524808, 345.19996643, -213.34531217
16given(0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699)345.19996643, -213.34531217, 131.85468478
17given(-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5), (0.80901699, 0.5, -0.30901699)690.3999176, -9.43E-6, 2.469E-5
18given(-1), (1), (-1)690.39993286, 3.052E-5, 690.39996338
19given(-0.5, -0.30901699, -0.80901699), (-0.30901699, -0.80901699, 0.5), (-0.80901699, 0.5, 0.30901699)903.7452392, 558.54529386, 345.199957
20given(-1), (1), (-1)690.39993286, 690.39993286
21given(-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5)345.19992648, -213.34530634, 131.85466952
22given(0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.80901699), (0.30901699, -0.80901699, -0.5)-5.83E-6, 1.526E-5, 690.39997281
23given(-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699), (0.5, -0.30901699, -0.80901699)345.19994174, -213.34529691, 558.54531855
24given(0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5), (-0.80901699, -0.5, -0.30901699)558.54528803, 345.19999112, 903.74526029
25given(-0.80901699, -0.5, -0.30901699), (-0.5, 0.30901699, 0.80901699), (-0.30901699, 0.80901699, -0.5)903.74522977, 131.85464483, 345.19997226
26given(-0.30901699, -0.80901699, 0.5), (-0.80901699, 0.5, 0.30901699), (-0.5, -0.30901699, -0.80901699)558.54526334, 345.199957, 903.74526972
27given(-0.30901699, 0.80901699, 0.5), (0.80901699, 0.5, -0.30901699), (-0.5, 0.30901699, -0.80901699)-3.995E-5, 2.469E-5, 690.39994812
28given(1), (-1), (-1)690.39996338, 690.39996338
29given(0.30901699, 0.80901699, -0.5), (0.80901699, -0.5, -0.30901699), (-0.5, -0.30901699, -0.80901699)131.854639, 345.20000638, 903.74526972
30given(0.30901699, -0.80901699, -0.5), (-0.80901699, -0.5, 0.30901699), (-0.5, 0.30901699, -0.80901699)690.39994229, 690.39993869, 690.39994812
31given(-1), (1), (-1)690.39990234, 690.39996338
32given(0.80901699, 0.5, -0.30901699), (-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5)-5.83E-6, 690.39994812, -9.43E-6
33given(-1), (-1), (1)690.39993286, 690.39996338, 3.052E-5
34given(-0.80901699, 0.5, 0.30901699), (-0.5, -0.30901699, -0.80901699), (-0.30901699, -0.80901699, 0.5)345.19992648, 903.74526972, 558.54529386
35given(-0.5, -0.30901699, 0.80901699), (-0.30901699, -0.80901699, -0.5), (0.80901699, -0.5, 0.30901699)345.19993591, 903.74527555, 131.85468478
36given(0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699)-213.34534269, 558.5452786, 345.19996643
37given(0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5)131.85465426, 345.19999695, -213.34531217
38given(0.80901699, 0.5, 0.30901699), (0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5)-213.34532743, 558.54531855, 345.19997226
39given(0.30901699, -0.80901699, 0.5), (-0.80901699, -0.5, -0.30901699), (0.5, -0.30901699, -0.80901699)345.1999606, 903.74526029, 558.54531855
40given(-0.5, 0.30901699, 0.80901699), (-0.30901699, 0.80901699, -0.5), (-0.80901699, -0.5, -0.30901699)131.85461431, 345.19997226, 903.74526029
41given(1), (-1), (-1)-3.052E-5, 690.39993286, 690.39996338
42given(0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699)-213.34533686, 131.85466952, 345.199957
43given(0.5, -0.30901699, 0.80901699), (0.30901699, -0.80901699, -0.5), (0.80901699, 0.5, -0.30901699)-1.526E-5, 690.39997281, 2.469E-5
44given(0.30901699, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699)-213.34534269, 131.85468478, 345.19999695
45given(0.80901699, -0.5, 0.30901699), (-0.5, -0.30901699, 0.80901699), (-0.30901699, -0.80901699, -0.5)131.85465426, 345.19996643, 903.74527555
46given(-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699)345.19993591, -213.34531217, 558.5452786
47given(0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699)-1.526E-5, -9.43E-6, 690.39993869
48given(1), (1), (1)-3.052E-5, 3.052E-5
49given(0.5, 0.30901699, 0.80901699), (-0.30901699, -0.80901699, 0.5), (0.80901699, -0.5, -0.30901699)-213.34533686, 558.54529386, 345.20000638
50given(1), (1), (1)-3.052E-5, 3.052E-5
51given(0.80901699, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699), (-0.30901699, -0.80901699, 0.5)345.19997586, -213.34530634, 558.54529386
52given(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)690.39990817, 1.526E-5, -9.43E-6
53given(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)345.1999606, -213.34529691, 131.85464483
54given(-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699)131.85461431, 345.19999112, -213.34529691
55given(0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5)-213.34532743, 131.85464483, 345.19999112
56given(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)131.854639, 345.199957, -213.34530634
57given(0.30901699, -0.80901699, -0.5), (0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.80901699)690.39994229, 2.469E-5, 1.526E-5
58given(-1), (-1), (1)690.39990234, 690.39996338
59given(-0.30901699, -0.80901699, 0.5), (0.80901699, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699)558.54526334, 345.20000638, -213.34530634
60given(-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699)-3.995E-5, 690.39993869, 1.526E-5

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Components

#1: Protein Peptide 2k


Mass: 43376.238 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: TGTQG loop was deleted, as there is no EM-density to support it's modelling
Source: (gene. exp.) Tick-borne encephalitis virus (STRAIN SOFJIN)
Production host: Tick-borne encephalitis virus (STRAIN SOFJIN)
References: UniProt: P07720
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tick-borne encephalitis virus (STRAIN SOFJIN) / Type: VIRUS / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Tick-borne encephalitis virus (STRAIN SOFJIN)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 66 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39000 / Symmetry type: POINT

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