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- EMDB-57016: consensus map; human 48S PIC on Kozak mRNA (Kozak_2) -

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Basic information

Entry
Database: EMDB / ID: EMD-57016
Titleconsensus map; human 48S PIC on Kozak mRNA (Kozak_2)
Map data
Sample
  • Complex: 48S PIC
Keywordstranslation initiation / 48S PIC / human / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
Authorsvon Loeffelholz O / Klaholz B
Funding support France, 4 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE11-0003-01 France
Agence Nationale de la Recherche (ANR)ANR 20-SFRI-0012 France
Laboratories of Excellence (LabEx)ANR-10-LABX-0036_NETRNA France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-0005 France
CitationJournal: Nat Commun / Year: 2026
Title: Translation initiation by the Kozak mRNA sequence is based on a conformational readout on the ribosome.
Authors: Ottilie von Loeffelholz / Charles Barchet / Samuel Holvec / Aida Abou Ramadan / Cristina Protuc / Anne Maglott-Roth / S Nimali T de Silva / Isabelle Hazemann / Bruno P Klaholz /
Abstract: The recognition mechanism of Kozak mRNA, typically comprising purines in the -3 and +4 positions flanking the AUG start codon, has remained enigmatic for decades. To address this fundamental function ...The recognition mechanism of Kozak mRNA, typically comprising purines in the -3 and +4 positions flanking the AUG start codon, has remained enigmatic for decades. To address this fundamental function in eukaryotes during translation initiation, we analysed several cryo-EM structures of human 48S preinitiation complexes with mRNA sequences differing in Kozak activity revealing distinct modes of recognition. The pre-codon triplet forms a fan-like intercalation into the 18S ribosomal RNA (rRNA), while a -3 pyrimidine destabilizes ternary complex positioning. Specificity towards the +4 purine is achieved beyond a single residue recognition by mutual conformational adaptations of eIF1A, mRNA and rRNA that involve the insertion of a reading head in which decoding residue A1825 (rRNA) stacks with the A-site codon to stabilize the fully accommodated state. Hence, instead of relying on base pairing as in bacteria, the specific recognition of the Kozak sequence on eukaryotic ribosomes is based on an induced-fit mechanism that triggers a conformational readout of the mRNA.
History
DepositionMar 3, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57016.png

Downloads & links

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Map

FileDownload / File: emd_57016.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.72 Å/pix.
x 480 pix.
= 345.6 Å		0.72 Å/pix.
x 480 pix.
= 345.6 Å		0.72 Å/pix.
x 480 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.19
Minimum - Maximum-12.537182 - 22.484684000000001
Average (Standard dev.)0.000000000000332 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_57016_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_57016_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 : 48S PIC

EntireName: 48S PIC
Components
  • Complex: 48S PIC

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Supramolecule #1: 48S PIC

SupramoleculeName: 48S PIC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#50
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.8 MDa

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.1) / Number images used: 36575
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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