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- EMDB-77122: Cryo-EM map of the mature SLEV, full particle -

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Basic information

Entry
Database: EMDB / ID: EMD-77122
TitleCryo-EM map of the mature SLEV, full particle
Map datapost-processed map of full virion particle solved at 3.6 A with imposed icosahedral symmetry made with the original map and mask
Sample
  • Virus: St. Louis encephalitis virus
KeywordsSLEV / cryo-EM / full particle / VIRUS
Biological speciesSt. Louis encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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 12, 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_77122.png

Downloads & links

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Map

FileDownload / File: emd_77122.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-processed map of full virion particle solved at 3.6 A with imposed icosahedral symmetry made with the original map and mask
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 540 pix.
= 598.023 Å		1.11 Å/pix.
x 540 pix.
= 598.023 Å		1.11 Å/pix.
x 540 pix.
= 598.023 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: 0.02
Minimum - Maximum-0.046028204 - 0.08639586
Average (Standard dev.)0.00061801344 (±0.006150389)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-270-270-270
Dimensions540540540
Spacing540540540
CellA=B=C: 598.023 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77122_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: original map of full virion particle after 3D-auto...

Fileemd_77122_additional_1.map
Annotationoriginal map of full virion particle after 3D-auto refine without post-processing with mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_77122_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_77122_half_map_2.map
Annotationhalf map 1
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

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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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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: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / 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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