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- EMDB-55068: CRYO-EM FOCUSED REFINEMENT MAP OF HUMAN 80S RIBOSOME WITH A/P/E-S... -

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Basic information

Entry
Database: EMDB / ID: EMD-55068
TitleCRYO-EM FOCUSED REFINEMENT MAP OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE
Map dataBody 1
Sample
  • Complex: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE
KeywordsCRYO-EM STRUCTURE / HUMAN / 80S / RIBOSOME / N1-METHYLPSEUDOURIDINE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsRajan KS / Yonath A
Funding support Israel, 1 items
OrganizationGrant numberCountry
The Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly Israel
CitationJournal: Nature / Year: 2026
Title: N-Methylpseudouridine directly modulates translation dynamics.
Authors: Batsheva Rozman / Karin Broennimann / K Shanmugha Rajan / Aharon Nachshon / Chiranjeet Saha / Tamar Arazi / Vishnu Mohan / Tamar Geiger / Clayton J Wollner / Justin M Richner / Eric Westhof ...Authors: Batsheva Rozman / Karin Broennimann / K Shanmugha Rajan / Aharon Nachshon / Chiranjeet Saha / Tamar Arazi / Vishnu Mohan / Tamar Geiger / Clayton J Wollner / Justin M Richner / Eric Westhof / Ada Yonath / Anat Bashan / Noam Stern-Ginossar /
Abstract: The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology. A critical feature of this approach is the ...The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology. A critical feature of this approach is the incorporation of the modified nucleoside N-methylpseudouridine (mΨ), which enhances antigen expression while reducing immunogenicity. However, a comprehensive understanding of how mΨ influences translation remains incomplete. Here we use ribosome profiling at the subcodon resolution to show that mΨ increases ribosome density on synthetic mRNAs, leading to higher protein production independent of innate immune activation or eIF2α phosphorylation. We find that mΨ directly slows ribosome movement in defined sequence contexts while simultaneously promoting translation initiation. Structural studies using cryo-electron microscopy reveal that mΨ alters interactions within the ribosomal decoding centre, providing a mechanistic basis for slowed elongation. Furthermore, by introducing synonymous recoding that disrupts the modification-mediated changes in elongation, we show that the mΨ-dependent enhancement of protein output is modulated by codon composition, and that mΨ impact is strongest in mRNAs containing non-optimal codons with uridines at the wobble position. Together, these findings demonstrate that mΨ directly modulates translation dynamics, thereby increasing protein yield from synthetic mRNAs in specific sequence contexts.
History
DepositionSep 16, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55068.png

Downloads & links

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Map

FileDownload / File: emd_55068.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody 1
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 395.76 Å		0.82 Å/pix.
x 480 pix.
= 395.76 Å		0.82 Å/pix.
x 480 pix.
= 395.76 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8245 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.0253475 - 0.050864566
Average (Standard dev.)-0.00023551068 (±0.0024036814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 395.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Halfmap for Body 2

Fileemd_55068_additional_1.map
AnnotationHalfmap for Body 2
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Additional map: Body 2

Fileemd_55068_additional_2.map
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Additional map: Body 4

Fileemd_55068_additional_3.map
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Fileemd_55068_additional_4.map
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Fileemd_55068_additional_5.map
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Fileemd_55068_additional_6.map
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Fileemd_55068_additional_7.map
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Fileemd_55068_additional_8.map
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Fileemd_55068_additional_9.map
AnnotationHalfmap for Body 4
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Half map: Halfmap for Body 1

Fileemd_55068_half_map_1.map
AnnotationHalfmap for Body 1
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Half map: Halfmap for Body 1

Fileemd_55068_half_map_2.map
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Sample components

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Entire : CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND ...

EntireName: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE
Components
  • Complex: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE

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Supramolecule #1: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND ...

SupramoleculeName: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#83
Details: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE
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: 7.6
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: 1.077 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.6 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: PDB ENTRY
PDB model - PDB ID:

8glp

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 121901
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5
FSC plot (resolution estimation)

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