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- EMDB-50624: LGTV TP21. Langat virus, strain TP21 -

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Basic information

Entry
Database: EMDB / ID: EMD-50624
TitleLGTV TP21. Langat virus, strain TP21
Map dataSharpened with deepEMchancer.
Sample
  • Virus: Langat virus (strain TP21)
    • Protein or peptide: Envelope protein E
    • Protein or peptide: Small envelope protein M
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsFlavivirus / Langat virus / recombinant virus / 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 / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase ...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 / 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 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 speciesLangat virus (strain TP21)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsBisikalo K / Rosendal E
Funding support Sweden, 1 items
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 SM / Lindgren M / Holoubek J / Svoboda P / Lappalainen A / Konighofer E / Mirgorodskaya E / Norden R / Morini F / Rosenbaum W / Ruzek D / Ahlgren U / ...Authors: Rosendal E / Bisikalo K / Willekens SM / 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 SJ / Nilsson E / Overby AK
History
DepositionJun 12, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50624.png

Downloads & links

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Map

FileDownload / File: emd_50624.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened with deepEMchancer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 756 pix.
= 733.32 Å		0.97 Å/pix.
x 756 pix.
= 733.32 Å		0.97 Å/pix.
x 756 pix.
= 733.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.1125385 - 1.9267309
Average (Standard dev.)0.004932732 (±0.047419827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions756756756
Spacing756756756
CellA=B=C: 733.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50624_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50624_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Langat virus (strain TP21)

EntireName: Langat virus (strain TP21)
Components
  • Virus: Langat virus (strain TP21)
    • Protein or peptide: Envelope protein E
    • Protein or peptide: Small envelope protein M
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Langat virus (strain TP21)

SupramoleculeName: Langat virus (strain TP21) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 31638 / Sci species name: Langat virus (strain TP21) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Diameter: 500.0 Å / T number (triangulation number): 3

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Macromolecule #1: Envelope protein E

MacromoleculeName: Envelope protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Langat virus (strain TP21)
Molecular weightTheoretical: 53.574301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SRCTHLENRD FVTGVQGTTR LTLVLELGGC VTVTADGKPS LDVWLDSIYQ ESPAQTREYC LHAKLTGTKV AARCPTMGPA TLPEEHQSG TVCKRDQSDR GWGNHCGLFG KGSIVTCVKF TCEDKKKATG HVYDVNKITY TIKVEPHTGE FVAANETHSG R KSASFTVS ...String:
SRCTHLENRD FVTGVQGTTR LTLVLELGGC VTVTADGKPS LDVWLDSIYQ ESPAQTREYC LHAKLTGTKV AARCPTMGPA TLPEEHQSG TVCKRDQSDR GWGNHCGLFG KGSIVTCVKF TCEDKKKATG HVYDVNKITY TIKVEPHTGE FVAANETHSG R KSASFTVS SEKTILTLGD YGDVSLLCRV ASGVDLAQTV VLALDKTHEH LPTAWQVHRD WFNDLALPWK HDGAEAWNEA GR LVEFGTP HAVKMDVFNL GDQTGVLLKS LAGVPVASIE GTKYHLKSGH VTCEVGLEKL KMKGLTYTVC DKTKFTWKRA PTD SGHDTV VMEVGFSGTR PCRIPVRAVA HGVPEVNVAM LITPNPTMEN NGGGFIEMQL PPGDNIIYVG DLNHQWFQKG SSIG RVLQK TRKGIERLTV LGEHAWDFGS VGGVMTSIGR AMHTVLGGAF NTLLGGVGFL PKILLGVAMA WLGLNMRNPT LSMGF LLSG GLVLAMTLGV GA

UniProtKB: Genome polyprotein

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Macromolecule #2: Small envelope protein M

MacromoleculeName: Small envelope protein M / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Langat virus (strain TP21)
Molecular weightTheoretical: 8.249828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VLIPSHAQRD LTGRGHQWLE GEAVKAHLTR VEGWVWKNKL FTLSLVMVAW LMVDGLLPRI LIVVVALALA PAYA

UniProtKB: Genome polyprotein

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Macromolecule #4: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / Number of copies: 6 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Details: VP-SFM growth medium, supplemented with rapamycin and glutamate.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1430 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 150000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 15306
Startup modelType of model: INSILICO MODEL / In silico model: Cryosparc Ab-Initio
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12857
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Avg.num./class: 6000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9foj:
LGTV TP21. Langat virus, strain TP21

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