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- PDB-9fk0: LGTV with TBEV prME -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9fk0
TitleLGTV with TBEV prME
Components
  • Genome polyprotein
  • Genome polyprotein,Envelope protein E
KeywordsVIRUS / Chimeric virus / Flavivirus / Tick-borne Encephalitis virus / Langat virus / recombinant virus
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / ribonucleoside triphosphate phosphatase activity / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / ribonucleoside triphosphate phosphatase activity / symbiont-mediated activation of host apoptosis / 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 entry into host cell / 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
Chem-CPL / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciestick-borne encephalitis virus-European subtype
Langat virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsBisikalo, K. / Rosendal, E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-05851 Sweden
CitationJournal: Biorxiv / Year: 2024
Title: The influence of the pre-membrane and envelope proteins on structure, pathogenicity and tropism of tick-borne encephalitis virus
Authors: Rosendal, E. / Bisikalo, K. / Willekens, S.M. / Lindgren, M. / Holoubek, J. / Svoboda, P. / Lappalainen, A. / Konighofer, E. / Mirgorodskaya, E. / Norden, R. / Morini, F. / Rosenbaum, W. / ...Authors: Rosendal, E. / Bisikalo, K. / Willekens, S.M. / Lindgren, M. / Holoubek, J. / Svoboda, P. / Lappalainen, A. / Konighofer, E. / Mirgorodskaya, E. / Norden, R. / Morini, F. / Rosenbaum, W. / Ruzek, D. / Ahlgren, U. / Anastasina, M. / Merits, A. / Butcher, S.J. / Nilsson, E. / Overby, A.K.
History
DepositionJun 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: em_admin / entity ...em_admin / entity / entity_name_com / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _em_admin.last_update / _entity.pdbx_description ..._em_admin.last_update / _entity.pdbx_description / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,69615
Polymers185,8756
Non-polymers5,8229
Water00
1
A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules

A: Genome polyprotein,Envelope protein E
B: Genome polyprotein,Envelope protein E
C: Genome polyprotein,Envelope protein E
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,501,783900
Polymers11,152,490360
Non-polymers349,294540
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Genome polyprotein,Envelope protein E


Mass: 53646.422 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) tick-borne encephalitis virus-European subtype, (gene. exp.) Langat virus (strain TP21)
Strain: 93/783 / Cell line (production host): A549 MAVS -/- / Production host: Homo sapiens (human) / References: UniProt: A0A7M3UFX3, UniProt: P29837
#2: Protein Genome polyprotein


Mass: 8311.854 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) tick-borne encephalitis virus-European subtype
Strain: 93/783 / Cell line (production host): A549 MAVS -/- / Production host: Homo sapiens (human) / References: UniProt: A0A7M3UFX3
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationY

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1LGTV with TBEV prMEVIRUSChimeric virus based on the Langat virus (LGTV) and Tick-borne Encephalitis virus (TBEV). prM and ectodomains of E are taken from TBEV (European subtype, strain 93/873), while the rest of the virus genome is from LGTV TP21.#1-#20MULTIPLE SOURCES
2Envelope protein ECOMPLEX#11RECOMBINANT
3Small envelope protein MCOMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12tick-borne encephalitis virus-European subtype2848310Chimeric virus (prME from TBEV)
22Langat virus (strain TP21)31638Chimeric virus (prME from TBEV)
33tick-borne encephalitis virus-European subtype2848310Chimeric virus (prME from TBEV)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Homo sapiens (human)9606A549 MAVS -/-
33Homo sapiens (human)9606A549 MAVS -/-
Details of virusEmpty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION
Virus shellDiameter: 500 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Details: VP-SFM growth medium, supplemented with rapamycin and glutamate.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.27 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 32122

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9ISOLDEmodel refinement
10PHENIXmodel refinement
11Cootmodel refinement
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 97855
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18724 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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