9XAD | pdb_00009xad

Cryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 WT) from Chaetomium thermophilum, state Rrp12-A2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.0 of the entry. See complete history

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: 1,487.62 kDa 
  • Atom Count: 84,804 
  • Modeled Residue Count: 8,038 
  • Deposited Residue Count: 9,895 
  • Unique protein chains: 34
  • 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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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))
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s5-like proteinC [auth I]212Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S1Z0 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6D [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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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7E [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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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8F [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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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinG [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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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinH [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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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12I [auth P]144Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SHH9 (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 S13-like proteinJ [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: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinK [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: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s15-like proteinL [auth S]153Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S084 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-like proteinM [auth T]143Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SBR7 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal proteinN [auth V]156Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S6J7 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinO [auth W]153Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SFK8 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-like proteinP [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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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s23-like proteinQ [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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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24R [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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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S25S [auth c]99Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S1Y9 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein s27-like proteinT [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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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-like proteinU [auth f]68Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S9M9 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30V [auth h]62Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27a-like proteinW [auth i]154Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S2X5 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Trm112Y [auth 0]127Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Methyltransferase-like proteinZ [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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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Bms1-type G domain-containing proteinAA [auth 2]830Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RZ98 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1BA [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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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Bystin-like proteinCA [auth 4]480Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S5J4 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative low-temperature viability proteinDA [auth 5]445Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 12-like conserved domain-containing proteinEA [auth 7]1,235Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S052 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2FA [auth SA]285Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RYF9 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5GA [auth SC]263Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-like proteinHA [auth SR]143Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S871 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-like proteinIA [auth SV]98Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SI21 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 24
MoleculeChains LengthOrganismImage
18S rRNAX [auth A]1,796Thermochaetoides thermophila
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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