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- EMDB-66691: Cryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 Mut ) from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66691
TitleCryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 Mut ) from Chaetomium thermophilum, state Rio2-C*
Map datalocal resolution filtered map using Relion
Sample
  • Complex: pre-40S ribosome, state Rio2-C*
Keywords90S pre-ribosome / Rrp12 / Enp1 / ribosome biogenesis / RIBOSOME
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsLau B / Li Y / Zhu J / Fisher P / Hong X / Yuan R / Beckmann R / Hurt E / Cheng J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2026
Title: Nucleoplasmic checkpoint of the 40S ribosomal decoding center maturation.
Authors: Benjamin Lau / Yi Li / Jingyi Zhu / Xianwen Ye / Paulina Fischer / Xiaying Hong / Rui Yuan / Roland Beckmann / Ed Hurt / Jingdong Cheng /
Abstract: The decoding center (DC) is a key ribosomal structure for accurate translation, assembled in a multi-step process that starts on nucleolar pre-ribosomes and ends in the cytoplasm. While late ...The decoding center (DC) is a key ribosomal structure for accurate translation, assembled in a multi-step process that starts on nucleolar pre-ribosomes and ends in the cytoplasm. While late cytoplasmic steps and their checkpoint mechanisms are well characterized, the regulation of early nucleoplasmic DC assembly is unclear. Here, we show that the essential assembly factor Rrp12 plays a central coordinating role. Using Chaetomium thermophilum and cryo-electron microscopy analyses of fifteen pre-40S intermediates, we demonstrate that Rrp12 C terminus truncation: (1) inhibits release of the Utp14-Dhr1 pair, (2) displaces Tsr1, (3) promotes premature stabilization of h28, and (4) prevents h44 formation. These defects impair final 18S rRNA processing and prematurely activate the quality control kinase Rio1. Our results reveal a nucleoplasmic checkpoint during DC formation and establish Rrp12 as a critical regulator ensuring accurate assembly and orderly ribosome maturation.
History
DepositionOct 22, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66691.png

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Map

FileDownload / File: emd_66691.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map using Relion
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 376.2 Å		1.05 Å/pix.
x 360 pix.
= 376.2 Å		1.05 Å/pix.
x 360 pix.
= 376.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.13757847 - 0.26217952
Average (Standard dev.)-0.00012458295 (±0.0061495057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 376.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_66691_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_66691_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pre-40S ribosome, state Rio2-C*

EntireName: pre-40S ribosome, state Rio2-C*
Components
  • Complex: pre-40S ribosome, state Rio2-C*

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Supramolecule #1: pre-40S ribosome, state Rio2-C*

SupramoleculeName: pre-40S ribosome, state Rio2-C* / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#57
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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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: 7.4
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: 44.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION / Details: Relion / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rxu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 3017
Initial angle assignmentType: OTHER / Software - Name: RELION / Details: Relion
Final angle assignmentType: OTHER / Software - Name: RELION / Details: Relion
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6g18


Chain - Source name: PDB / Chain - Initial model type: experimental model

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