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- EMDB-56556: CLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES I... -

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Basic information

Entry
Database: EMDB / ID: EMD-56556
TitleCLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES IN COMPLEX WITH MRNA AND TRNA
Map dataConsensus map
Sample
  • Complex: CLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES IN COMPLEX WITH MRNA AND TRNA
KeywordsCRYO-EM / LD32CS1C1 / SNORNA / COMPLEX WITH MRNA AND TRNA / RIBOSOME
Biological speciesLeishmania donovani (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.18 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: Nat Commun / Year: 2026
Title: A small nucleolar RNA dictates the structure and function of translating ribosomes in Leishmania.
Authors: K Shanmugha Rajan / Saurav Aryal / Sharanya Murugeshan / Yinzhou Zhu / Anat Bashan / Mika Olami / Hava Madmoni / Yuko Nobe / Tirza Doniger / Smadar Cohen-Chalamish / Eric Prina / Pascale ...Authors: K Shanmugha Rajan / Saurav Aryal / Sharanya Murugeshan / Yinzhou Zhu / Anat Bashan / Mika Olami / Hava Madmoni / Yuko Nobe / Tirza Doniger / Smadar Cohen-Chalamish / Eric Prina / Pascale Pescher / Tom Beneke / Masato Taoka / Christopher L Holley / Ron Unger / Gerald F Späth / Ada Yonath / Shulamit Michaeli /
Abstract: The most common rRNA modification is 2'-O-methylation. Here, we determine the landscape of 2'-O-methylation in Leishmania, a parasite that cycles between two different hosts, insect and mammalian. We ...The most common rRNA modification is 2'-O-methylation. Here, we determine the landscape of 2'-O-methylation in Leishmania, a parasite that cycles between two different hosts, insect and mammalian. We find two 2'-O-methylated positions that are differentially modified during the parasite's two life stages. The deposition of these modifications is guided by snoRNAs. When we perform cytosine base-editing of the snoRNA responsible for guiding one of the two stage-regulated modifications, Am479, we fail to detect ribosomes lacking this modification, suggesting that it is essential. To better understand the role of the snoRNA and its guided modification, we determine the cryo-EM structures of ribosomes from cells overexpressing the guiding snoRNA and compare them to ribosomes from the parental strain. We do not find structural changes around Am479 or in the small subunit rRNA, but observe a difference in H68 of the large subunit rRNA due to a second base-pairing interaction, suggesting a potential chaperone activity for the snoRNA. Based on these results, translatome and tRNA analysis, we propose a mechanism whereby changes in ribosome structure affect the release of specific tRNAs, which correlate with changes in translation of only a subset of mRNAs.
History
DepositionFeb 4, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56556.png

Downloads & links

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Map

FileDownload / File: emd_56556.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.00982419 - 0.046829514
Average (Standard dev.)0.0001746262 (±0.0024788233)
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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Half map: Halfmap for Consensus map

Fileemd_56556_half_map_1.map
AnnotationHalfmap for Consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap for Consensus map

Fileemd_56556_half_map_2.map
AnnotationHalfmap for Consensus 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 : CLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES I...

EntireName: CLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES IN COMPLEX WITH MRNA AND TRNA
Components
  • Complex: CLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES IN COMPLEX WITH MRNA AND TRNA

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Supramolecule #1: CLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES I...

SupramoleculeName: CLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES IN COMPLEX WITH MRNA AND TRNA
type: complex / ID: 1 / Parent: 0
Details: CLASS-6_APE_CRYO-EM CONSENSUS MAP OF LD32CS1C1 EDITED RIBOSOMES IN COMPLEX WITH MRNA AND TRNA
Source (natural)Organism: Leishmania donovani (eukaryote)

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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: 0.929 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: 0.6 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 224661
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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