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- EMDB-64263: CryoEM structure of Western equine encephalitis virus California ... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-64263
TitleCryoEM structure of Western equine encephalitis virus California VLP in complex with VLDLR-LA3
Map data
Sample
  • Virus: Western equine encephalitis virus
KeywordsWEEV / VLP / E2-E1 glycoproteins / VIRAL PROTEIN
Biological speciesWestern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsLiang SJ / Lou ZY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural insights into VLDLR recognition by Western Equine Encephalitis Virus
Authors: Liang SJ / Lou ZY
History
DepositionApr 20, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64263.png

Downloads & links

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Map

FileDownload / File: emd_64263.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.036874 - 1.4619713
Average (Standard dev.)0.002527961 (±0.04747694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64263_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64263_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 : Western equine encephalitis virus

EntireName: Western equine encephalitis virus
Components
  • Virus: Western equine encephalitis virus

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Supramolecule #1: Western equine encephalitis virus

SupramoleculeName: Western equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11039 / Sci species name: Western equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 169438
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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