[English] 日本語
Yorodumi
- EMDB-55387: Cryo-EM structure of arabidopsis translating ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55387
TitleCryo-EM structure of arabidopsis translating ribosome
Map data
Sample
  • Complex: 60S LSU Arabidopsis (root) ribosome complex
KeywordsArabidopsis / Ribosome / CryoEM
Biological speciesArabidopsis (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsKarki S / Paavilainen V
Funding support United States, Finland, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132649[PVO1] United States
Academy of Finland338836 and 314672 Finland
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of the Arabidopsisthaliana ribosome in translating and non-translating states.
Authors: Sudeep Karki / Xun Lu / Anja O Paatero / Raili Ruonala / Dale Tranter / Sergey Guryanov / Shahid Rehan / Eva Hellmann / Anders Haakonsson / Sarah J Butcher / Juha T Huiskonen / Tommi ...Authors: Sudeep Karki / Xun Lu / Anja O Paatero / Raili Ruonala / Dale Tranter / Sergey Guryanov / Shahid Rehan / Eva Hellmann / Anders Haakonsson / Sarah J Butcher / Juha T Huiskonen / Tommi Kajander / Yrjö Helariutta / Ville O Paavilainen /
Abstract: Translational control of mRNA expression underpins much of post-transcriptional gene expression driving developmental processes in eukaryotes. How ribosomal mRNA translation is executed in plants may ...Translational control of mRNA expression underpins much of post-transcriptional gene expression driving developmental processes in eukaryotes. How ribosomal mRNA translation is executed in plants may be especially important for adapting to an ever-changing environment. Arabidopsis thaliana is the main genetic model organism in plant science, yet structural insights into developmental processes where ribosomal gene expression plays important roles currently remain lacking. Here, we present cryoelectron microscopy (cryo-EM) structures of the Arabidopsis cytosolic ribosome in both translating and non-translating states, which together provide new structural details into how translation of cytosolic mRNAs is coordinated. Our structures reveal detailed information on the interactions of tRNAs, mRNA, and the nascent polypeptide with subunits of the actively translating 80S ribosome and the role of ribosomal RNA methylation in stabilizing ribosomal subunits. The structures provide a foundation for interpreting the functional effects of many mutations of ribosomal proteins affecting phenotypic effects for plant tissue development.
History
DepositionOct 15, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55387.png

Downloads & links

-
Map

FileDownload / File: emd_55387.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 540 pix.
= 453.6 Å		0.84 Å/pix.
x 540 pix.
= 453.6 Å		0.84 Å/pix.
x 540 pix.
= 453.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.1876808 - 0.47285447
Average (Standard dev.)0.0022050624 (±0.02297733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 453.59998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_55387_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_55387_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 60S LSU Arabidopsis (root) ribosome complex

EntireName: 60S LSU Arabidopsis (root) ribosome complex
Components
  • Complex: 60S LSU Arabidopsis (root) ribosome complex

-
Supramolecule #1: 60S LSU Arabidopsis (root) ribosome complex

SupramoleculeName: 60S LSU Arabidopsis (root) ribosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#44
Source (natural)Organism: Arabidopsis (plant)
Molecular weightTheoretical: 4.3 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

-
Sample preparation

BufferpH: 7.4
Details: 50 mM Hepes, pH 7.4, 5 mM MgAc, 100 mM KAc, pH 7.5, 1 mM DTT, Complete protease inhibitor
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU (ver. v2.12.1)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 24.512 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 54325
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more