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- EMDB-77099: Cryo-EM structure of the mature SLEV, asymmetric unit -

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Basic information

Entry
Database: EMDB / ID: EMD-77099
TitleCryo-EM structure of the mature SLEV, asymmetric unit
Map datapost-processed map of the ASU, b-factor of -231.8
Sample
  • Virus: St. Louis encephalitis virus
    • Protein or peptide: Envelope Protein
    • Protein or peptide: Membrane protein
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
KeywordsSLEV / cryo-EM / asymmetric unit / VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell perinuclear region of cytoplasm ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / 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 / Immunoglobulin E-set / helicase superfamily c-terminal domain / 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 speciesSt. Louis encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGuimaraes SL / Marques RE / Coimbra LD / Benedetti C
Funding support Brazil, 1 items
OrganizationGrant numberCountry
Other private Brazil
CitationJournal: To Be Published
Title: THE STRUCTURES OF MATURE AND IMMATURE ST. LOUIS ENCEPHALITIS VIRUS REVEALS KEY HISTIDINE RESIDUES FOR VIRUS FITNESS
Authors: Guimaraes SL / Marques RE / Coimbra LD / Benedetti C
History
DepositionMay 11, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77099.png

Downloads & links

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Map

FileDownload / File: emd_77099.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-processed map of the ASU, b-factor of -231.8
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 220 pix.
= 243.639 Å		1.11 Å/pix.
x 220 pix.
= 243.639 Å		1.11 Å/pix.
x 220 pix.
= 243.639 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.10745 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.13725087 - 0.24682648
Average (Standard dev.)0.0006346575 (±0.014107213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 243.639 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77099_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: original unsharpened ASU map

Fileemd_77099_additional_1.map
Annotationoriginal unsharpened ASU map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ASU half-map 1

Fileemd_77099_half_map_1.map
AnnotationASU half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ASU half-map 2

Fileemd_77099_half_map_2.map
AnnotationASU half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : St. Louis encephalitis virus

EntireName: St. Louis encephalitis virus
Components
  • Virus: St. Louis encephalitis virus
    • Protein or peptide: Envelope Protein
    • Protein or peptide: Membrane protein
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: St. Louis encephalitis virus

SupramoleculeName: St. Louis encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 11080 / Sci species name: St. Louis encephalitis virus / Sci species strain: BeH355964 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope Protein

MacromoleculeName: Envelope Protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: St. Louis encephalitis virus / Strain: BeH355964
Molecular weightTheoretical: 54.025055 KDa
SequenceString: FNCLGTSNRD FVEGASGATW IDLVLEGGSC VTVMAPEKPT LDFKVMKMEA TELATVREYC YEATLDTLST VARCPTTGEA HNTKRSDLT FVCKRDVVDR GWGNGCGLFG KGSIDTCAKF TCKNKATGKT ILRENIKYEV AIFVHGSTDS TSHGNYSEQI G KNQAARFT ...String:
FNCLGTSNRD FVEGASGATW IDLVLEGGSC VTVMAPEKPT LDFKVMKMEA TELATVREYC YEATLDTLST VARCPTTGEA HNTKRSDLT FVCKRDVVDR GWGNGCGLFG KGSIDTCAKF TCKNKATGKT ILRENIKYEV AIFVHGSTDS TSHGNYSEQI G KNQAARFT ISPQAPSFTA NMGEYGTVTI DCEARSGINT EDYYVFTVKE KSWLVNRDWF HDLNLPWTSP ATTDWRNRET LV EFEEPHA TKQTVVALGS QEGALHTALA GAIPATVSSS TLTLQSGHLK CRAKLDKVKI KGTTYGMCDS AFTFSKNPAD TGH GTVIVE LQYTGSNGPC RVPISVTANL MDLTPVGRLV TVNPFISTGG ANNKVMIEVE PPFGDSYIVV GRGTTQINYH WHKE GSSIG KALATTWKGA QRLAVLGDTA WDFGSIGGVF NSIGKAVHQV FGGAFRTLFG GMSWITQGLL GALLLWMGLQ ARDRS ISLT LLAVGGILIF LATSVQ

UniProtKB: Genome polyprotein

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Macromolecule #2: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: St. Louis encephalitis virus / Strain: BeH355964
Molecular weightTheoretical: 8.354722 KDa
SequenceString:
SISVQHHGDS TLATKNTPWL DTVKTTKYLT KVENWVLRNP GYALVALAIG WMLGSNNTQR VVFVIMLMLI APAYS

UniProtKB: Genome polyprotein

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 9 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / 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: 7.4
Sugar embeddingMaterial: Water
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 631158
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4)
Details: The 49,349 viral particles were further processed through localized reconstruction, yielding a subset of 1,172,175 subparticles for the final reconstruction
Number images used: 49349
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: RELION (ver. 4)
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: RIGID BODY FIT
Output model

PDB-13jv:
Cryo-EM structure of the mature SLEV, asymmetric unit

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