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- EMDB-56229: Body of small subunit from the composite map of 80S ribosomes fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-56229
TitleBody of small subunit from the composite map of 80S ribosomes from primary B-cells infected with WT M81 Epstein-Barr virus.
Map dataBody of small subunit from the composite map of 80S ribosomes from primary B-cells infected with WT M81 Epstein-Barr virus.
Sample
  • Complex: 80S ribosome of primary B-cells infected with WT EBV M81
KeywordsSSU / ribosome / B-cells / EBV / epstein barr / M81
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsFedorenko A / Bashan A / Yonath A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: An Epstein-Barr virus-encoded snoRNA directs 2-O-methylation of human rRNAs to control translation and the viral lytic switch
Authors: Yarden D / Beata EJ
History
DepositionJan 6, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56229.png

Downloads & links

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Map

FileDownload / File: emd_56229.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody of small subunit from the composite map of 80S ribosomes from primary B-cells infected with WT M81 Epstein-Barr virus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 395.52 Å		0.82 Å/pix.
x 480 pix.
= 395.52 Å		0.82 Å/pix.
x 480 pix.
= 395.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.04810689 - 0.14806488
Average (Standard dev.)0.0001323752 (±0.0021700675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: 2 Half map of the small subunit body...

Fileemd_56229_half_map_1.map
Annotation2 Half map of the small subunit body from the composite map of 80S ribosomes.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 1 Half map of the small subunit body...

Fileemd_56229_half_map_2.map
Annotation1 Half map of the small subunit body from the composite map of 80S ribosomes.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S ribosome of primary B-cells infected with WT EBV M81

EntireName: 80S ribosome of primary B-cells infected with WT EBV M81
Components
  • Complex: 80S ribosome of primary B-cells infected with WT EBV M81

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Supramolecule #1: 80S ribosome of primary B-cells infected with WT EBV M81

SupramoleculeName: 80S ribosome of primary B-cells infected with WT EBV M81
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#78
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6305 / Average exposure time: 15.8 sec. / Average electron dose: 37.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 178121
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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