[English] 日本語
Yorodumi
- EMDB-17236: CRYO-EM FOCUSED REFINEMENT MAP OF LEISHMANIA MAJOR 80S RIBOSOME :... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17236
TitleCRYO-EM FOCUSED REFINEMENT MAP OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN
Map dataBody 1 for focused refinement
Sample
  • Complex: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
KeywordsCRYO-EM / LEISHMANIA MAJOR / RIBOSOME / TRANSLATION
Biological speciesLeishmania major (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsRajan KS / Yonath A
Funding support Israel, European Union, 2 items
OrganizationGrant numberCountry
Israel Science Foundation Israel
European Research Council (ERC)European Union
CitationJournal: Cell Rep / Year: 2024
Title: Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification.
Authors: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / ...Authors: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / Aliza Fedorenko / Tanaya Bose / Ella Zimermann / Eric Prina / Noa Aharon-Hefetz / Yitzhak Pilpel / Toshiaki Isobe / Ron Unger / Gerald F Späth / Ada Yonath / Shulamit Michaeli /
Abstract: Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the ...Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function. To decipher the molecular mechanism of this phenotype, we determine the structure of ribosomes lacking the single Ψ and its parental strain at ∼2.4-3 Å resolution using cryo-EM. Our findings demonstrate the significance of a single Ψ on H69 to its structure and the importance for its interactions with helix 44 and specific tRNAs. Our study suggests that rRNA modification affects translation of mRNAs carrying codon bias due to selective accommodation of tRNAs by the ribosome. Based on the high-resolution structures, we propose a mechanism explaining how the ribosome selects specific tRNAs.
History
DepositionApr 27, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17236.png

Downloads & links

-
Map

FileDownload / File: emd_17236.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody 1 for focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.025064344 - 0.098021835
Average (Standard dev.)-0.00007035187 (±0.003201602)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Body 3 for focused refinement

Fileemd_17236_additional_1.map
AnnotationBody 3 for focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Body 2 for focused refinement

Fileemd_17236_additional_2.map
AnnotationBody 2 for focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map2 for Body 1 of focused refinement

Fileemd_17236_half_map_1.map
AnnotationHalf map2 for Body 1 of focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map1 for Body 1 of focused refinement

Fileemd_17236_half_map_2.map
AnnotationHalf map1 for Body 1 of focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1

EntireName: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
Components
  • Complex: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1

-
Supramolecule #1: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1

SupramoleculeName: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#85
Details: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
Source (natural)Organism: Leishmania major (eukaryote)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5t2a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212912
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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