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- EMDB-55216: Focus refined 60S map of WT-HEK 80S ribosome bound to TISU mRNA (... -

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Basic information

Entry
Database: EMDB / ID: EMD-55216
TitleFocus refined 60S map of WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)
Map dataPostprocesed 60S map obtained after Multibody refinement job of RELION.
Sample
  • Complex: Focus refined 60S map of WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)
Keywords80S Ribosome / TISU mRNA / Human / eS26 / WT-HEK / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHiregange DG / Fraticelli D / Bashan A / Yonath A / Dikstein R
Funding support1 items
OrganizationGrant numberCountry
Other privateTHE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY
CitationJournal: Nat Commun / Year: 2026
Title: Structural and molecular basis of specialized translation mediated by the ribosome mRNA-binding channel.
Authors: Davide Fraticelli / Disha Gajanan Hiregange / Benjamin Weiss / Ariel Ogran / Tal Havkin-Solomon / Irene Martinez Roman / Anat Bashan / Ada Yonath / Rivka Dikstein /
Abstract: The ribosome mRNA channel is central to translation, yet its role in regulatory mechanisms remains unclear. Using cryo-EM of human ribosomal complexes bound to Kozak and TISU mRNAs from wild-type (WT) ...The ribosome mRNA channel is central to translation, yet its role in regulatory mechanisms remains unclear. Using cryo-EM of human ribosomal complexes bound to Kozak and TISU mRNAs from wild-type (WT) and RPS26/eS26 mutant (RPS26dC) cells, we demonstrate that both RPS26/eS26 and mRNA adopt distinct conformations, explaining the opposing effects of RPS26dC on their activity. Translatome studies of WT and RPS26dC reveal AUG-context-dependent changes in 48S and 80S initiation complexes and slower scanning. Downregulated mRNAs are enriched for specific AUG-upstream nucleotides and a -1-cytosine contacting 18S rRNA G1207, an interaction lost in RPS26dC. Strongly affected transcripts include replication-dependent histones, which, despite short 5'UTRs and suboptimal Kozak, exhibit robust translation activity that is RPS26/eS26-dependent. We identify a translational enhancer in the H2B 5'UTR (-16 to -9) overlapping predicted RPS26/eS26-binding sites, with a distinct ribosome-bound conformation. Exploiting these features, we engineered a high-efficiency translational cassette with minimal leaky scanning. These findings underscore the role of the ribosome's mRNA channel in selective translation and its therapeutic potential.
History
DepositionSep 27, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55216.png

Downloads & links

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Map

FileDownload / File: emd_55216.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocesed 60S map obtained after Multibody refinement job of RELION.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 404.16 Å		0.84 Å/pix.
x 480 pix.
= 404.16 Å		0.84 Å/pix.
x 480 pix.
= 404.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.03070207 - 0.06115597
Average (Standard dev.)0.00018511916 (±0.0019740206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 404.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of 60S map obtained after Multibody...

Fileemd_55216_half_map_1.map
AnnotationHalf map of 60S map obtained after Multibody refinement job of RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of 60S map obtained after Multibody...

Fileemd_55216_half_map_2.map
AnnotationHalf map of 60S map obtained after Multibody refinement job of RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Focus refined 60S map of WT-HEK 80S ribosome bound to TISU mRNA (...

EntireName: Focus refined 60S map of WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)
Components
  • Complex: Focus refined 60S map of WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)

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Supramolecule #1: Focus refined 60S map of WT-HEK 80S ribosome bound to TISU mRNA (...

SupramoleculeName: Focus refined 60S map of WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#80
Source (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: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 74646
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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