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- EMDB-77127: Cryo-EM map of the immature SLEV, full particle -

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Basic information

Entry
Database: EMDB / ID: EMD-77127
TitleCryo-EM map of the immature SLEV, full particle
Map datapost-processed map obtained with the original map from 3D-auto-refine and mask
Sample
  • Virus: St. Louis encephalitis virus
KeywordsSLEV / cryo-EM / asymmetric unit / VIRUS
Biological speciesSt. Louis encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 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_77127.png

Downloads & links

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Map

FileDownload / File: emd_77127.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-processed map obtained with the original map from 3D-auto-refine and mask
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 700 pix.
= 775.215 Å		1.11 Å/pix.
x 700 pix.
= 775.215 Å		1.11 Å/pix.
x 700 pix.
= 775.215 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: 0.01
Minimum - Maximum-0.027016988 - 0.043350097
Average (Standard dev.)0.00020503106 (±0.002876452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 775.215 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77127_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: original map obtained in 3D-auto-refine with imposed icosahedral...

Fileemd_77127_additional_1.map
Annotationoriginal map obtained in 3D-auto-refine with imposed icosahedral symmetry, before post-processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_77127_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_77127_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: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4)
Details: somehow the FSC graphic in the validation analysis did not show the reported resolution described here (7.1 A). Also in next page, in Resolution estimates, the table does not include the ...Details: somehow the FSC graphic in the validation analysis did not show the reported resolution described here (7.1 A). Also in next page, in Resolution estimates, the table does not include the Reported by author 7.1 A resolution
Number images used: 50745
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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