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- EMDB-48049: Octopus ribosome, empty 80S -

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Basic information

Entry
Database: EMDB / ID: EMD-48049
TitleOctopus ribosome, empty 80S
Map datasharpened map
Sample
  • Complex: Octopus ribosome, hybrid state
KeywordsOctopus ribosone / RIBOSOME
Biological speciesOctopus (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGao J / Yip MCJ / Han R / Grearson A / Shao S / Lee ASY
Funding support United States, 1 items
OrganizationGrant numberCountry
David and Lucile Packard Foundation United States
CitationJournal: Curr Biol / Year: 2026
Title: Evolution of a core ribosomal innovation in octopus.
Authors: Rishav Mitra / Richard Han / Trey J Scott / Anik G Grearson / Jessica A Willi / Christina G Liu / Hyeongju Kim / Michael C Jewett / Nicholas W Bellono / Amy S Y Lee /
Abstract: Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations within the ancient molecular machines that execute the central dogma. Octopuses ...Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations within the ancient molecular machines that execute the central dogma. Octopuses exhibit complex nervous systems and sophisticated behaviors that rival vertebrates but via an entirely divergent evolutionary history. Here, we serendipitously discovered that octopus ribosomes contain a structural break in the core ribosomal RNA that is unique among all animals. This break site enhances translation fidelity to reduce miscoding and subsequent protein aggregation, even when engineered into evolutionarily distant bacterial ribosomes. Furthermore, high-fidelity translation by octopus ribosomes supports proteomic stability during extensive RNA editing observed in cephalopods, suggesting synergy between distinct non-canonical modes of gene regulation. This adaptation emerged in recently derived octopuses with expanded nervous systems, thereby revealing a mechanism that could broadly support the evolution of novel organismal traits.
History
DepositionNov 22, 2024-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48049.png

Downloads & links

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Map

FileDownload / File: emd_48049.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.057
Minimum - Maximum-0.16390479 - 0.28041482
Average (Standard dev.)0.00041354162 (±0.009132628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_48049_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Half map: half map 2

Fileemd_48049_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_48049_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Octopus ribosome, hybrid state

EntireName: Octopus ribosome, hybrid state
Components
  • Complex: Octopus ribosome, hybrid state

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Supramolecule #1: Octopus ribosome, hybrid state

SupramoleculeName: Octopus ribosome, hybrid state / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Octopus (invertebrata)

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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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

10181

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30629
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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