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- EMDB-55215: WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) consensus map -

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Basic information

Entry
Database: EMDB / ID: EMD-55215
TitleWT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) consensus map
Map dataPostprocesed consensus 3D refinement map of 80S ribosome obtained after polishing, and was used for aligning the Focus refined map obtained from Multibody refinement job of RELION.
Sample
  • Complex: WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) consensus map
Keywords80S Ribosome / TISU mRNA / Human / eS26 / WT-HEK / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHiregange DG / Fraticelli D / Bashan A / Yonath A / Dikstein R
Funding support Israel, 1 items
OrganizationGrant numberCountry
Other privateTHE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY Israel
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_55215.png

Downloads & links

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Map

FileDownload / File: emd_55215.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocesed consensus 3D refinement map of 80S ribosome obtained after polishing, and was used for aligning the Focus refined map obtained from 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-0.028632507 - 0.056007348
Average (Standard dev.)0.00020787475 (±0.00212456)
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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Additional map: Non-postprocesed consensus 3D refinement map of 80S ribosome...

Fileemd_55215_additional_1.map
AnnotationNon-postprocesed consensus 3D refinement map of 80S ribosome obtained after polishing, and was used for aligning the Focus refined map obtained from 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 consensus 3D refinement map of...

Fileemd_55215_half_map_1.map
AnnotationHalf map of consensus 3D refinement map of 80S ribosome obtained after polishing, and was used for aligning the Focus refined map obtained from 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 consensus 3D refinement map of...

Fileemd_55215_half_map_2.map
AnnotationHalf map of consensus 3D refinement map of 80S ribosome obtained after polishing, and was used for aligning the Focus refined map obtained from 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 : WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) consensus map

EntireName: WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) consensus map
Components
  • Complex: WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) consensus map

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Supramolecule #1: WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) consensus map

SupramoleculeName: WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) consensus map
type: complex / ID: 1 / Parent: 0
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: 3.0 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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