9XAI | pdb_00009xai

Cryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum, state Tsr1-1*


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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Literature

Nucleoplasmic checkpoint of the 40S ribosomal decoding center maturation.

Lau, B.Li, Y.Zhu, J.Ye, X.Fischer, P.Hong, X.Yuan, R.Beckmann, R.Hurt, E.Cheng, J.

(2026) Cell Rep 45: 117545-117545

  • DOI: https://doi.org/10.1016/j.celrep.2026.117545
  • Primary Citation Related Structures: 
    9XA7, 9XA8, 9XA9, 9XAA, 9XAB, 9XAC, 9XAD, 9XAE, 9XAF, 9XAG, 9XAH, 9XAI, 9XAJ, 9XAK

  • PubMed 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 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.


  • Organizational Affiliation
    • Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany; Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 1,071.08 kDa 
  • Atom Count: 44,705 
  • Modeled Residue Count: 3,688 
  • Deposited Residue Count: 6,165 
  • Unique protein chains: 18
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1A [auth E]255Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S7T8 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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UniProt GroupG0S7T8
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4B [auth H]264Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S1A6 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
Explore G0S1A6 
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UniProt GroupG0S1A6
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6C [auth J]239Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RY43 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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UniProt GroupG0RY43
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7D [auth K]203Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S8C4 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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UniProt GroupG0S8C4
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8E [auth L]202Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RY45 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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UniProt GroupG0RY45
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinF [auth M]190Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S0Z4 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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UniProt GroupG0S0Z4
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinG [auth O]161Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SF00 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13-like proteinH [auth Q]151Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RZM9 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinI [auth R]150Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SFL1 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-like proteinJ [auth Z]130Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SHI0 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s23-like proteinK [auth a]145Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RY17 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24L [auth b]136Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for P0CU28 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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UniProt GroupP0CU28
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein s27-like proteinM [auth e]82Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S1S4 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30N [auth h]62Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Methyltransferase-like proteinP [auth 1]282Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SC37 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1Q [auth 3]259Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S3T2 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase RIO1R [auth 6]519Thermochaetoides thermophilaMutation(s): 0 
EC: 2.7.11.1 (PDB Primary Data), 3.6.1 (PDB Primary Data)
UniProt
Find proteins for G0S3J5 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Utp14S [auth 8]938Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S8Y4 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Reference Sequence
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Entity ID: 15
MoleculeChains LengthOrganismImage
pre-18SO [auth A]1,797Thermochaetoides thermophila
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-24
    Type: Initial release