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- PDB-9xai: Cryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 Mut) from C... -

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Basic information

Entry
Database: PDB / ID: 9xai
TitleCryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum, state Tsr1-1*
Components
  • (40S ribosomal protein ...) x 11
  • (Small ribosomal subunit protein ...) x 2
  • Methyltransferase-like protein
  • Pre-rRNA-processing protein PNO1
  • Ribosomal protein s27-like protein
  • Serine/threonine-protein kinase RIO1
  • Utp14
  • pre-18S
KeywordsRIBOSOME / 90S pre-ribosome / Rrp12 / Enp1 / ribosome biogenesis
Function / homology
Function and homology information


rRNA (guanine-N7)-methylation / rRNA (guanine) methyltransferase activity / 90S preribosome / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / methyltransferase activity / small-subunit processome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit ...rRNA (guanine-N7)-methylation / rRNA (guanine) methyltransferase activity / 90S preribosome / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / methyltransferase activity / small-subunit processome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / methylation / cytoplasmic translation / non-specific serine/threonine protein kinase / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Rio1 / : / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / Methyltransferase type 11 ...Serine/threonine-protein kinase Rio1 / : / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / Methyltransferase type 11 / Methyltransferase domain / : / RIO domain / Small-subunit processome, Utp14 / Utp14 protein / : / : / Eukaryotic type KH-domain (KH-domain type I) / K Homology domain, type 1 superfamily / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S7e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S8e / Ribosomal protein S27 / Ribosomal protein S24e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / K Homology domain / K homology RNA-binding domain / Tyrosine protein kinases specific active-site signature. / : / Tyrosine-protein kinase, active site / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S11 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / 40S ribosomal protein S13-like protein / 40S ribosomal protein s9-like protein / 40S ribosomal protein S4 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / 40S ribosomal protein S13-like protein / 40S ribosomal protein s9-like protein / 40S ribosomal protein S4 / Ribosomal protein s27-like protein / Serine/threonine-protein kinase RIO1 / Pre-rRNA-processing protein PNO1 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S7 / Uncharacterized protein / Methyltransferase-like protein / 40S ribosomal protein S11-like protein / 40S ribosomal protein S14-like protein / 40S ribosomal protein S22-like protein / Small ribosomal subunit protein eS24
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLau, B. / Li, Y. / Zhu, J. / Fischer, P. / Hong, X. / Yuan, R. / Beckmann, R. / Hurt, E. / Cheng, J.
Funding support1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Small ribosomal subunit protein eS1
H: 40S ribosomal protein S4
J: 40S ribosomal protein S6
K: 40S ribosomal protein S7
L: 40S ribosomal protein S8
M: 40S ribosomal protein s9-like protein
O: 40S ribosomal protein S11-like protein
Q: 40S ribosomal protein S13-like protein
R: 40S ribosomal protein S14-like protein
Z: 40S ribosomal protein S22-like protein
a: 40S ribosomal protein s23-like protein
b: Small ribosomal subunit protein eS24
e: Ribosomal protein s27-like protein
h: 40S ribosomal protein S30
A: pre-18S
1: Methyltransferase-like protein
3: Pre-rRNA-processing protein PNO1
6: Serine/threonine-protein kinase RIO1
8: Utp14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,071,08422
Polymers1,070,97019
Non-polymers1143
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Small ribosomal subunit protein ... , 2 types, 2 molecules Eb

#1: Protein Small ribosomal subunit protein eS1


Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S7T8
#12: Protein Small ribosomal subunit protein eS24 / 40S ribosomal protein S24


Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: P0CU28

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40S ribosomal protein ... , 11 types, 11 molecules HJKLMOQRZah

#2: Protein 40S ribosomal protein S4


Mass: 29800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S1A6
#3: Protein 40S ribosomal protein S6


Mass: 27490.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RY43
#4: Protein 40S ribosomal protein S7


Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S8C4
#5: Protein 40S ribosomal protein S8


Mass: 23102.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RY45
#6: Protein 40S ribosomal protein s9-like protein


Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S0Z4
#7: Protein 40S ribosomal protein S11-like protein


Mass: 18698.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SF00
#8: Protein 40S ribosomal protein S13-like protein


Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RZM9
#9: Protein 40S ribosomal protein S14-like protein


Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SFL1
#10: Protein 40S ribosomal protein S22-like protein


Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SHI0
#11: Protein 40S ribosomal protein s23-like protein


Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RY17
#14: Protein 40S ribosomal protein S30


Mass: 6917.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)

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Protein , 5 types, 5 molecules e1368

#13: Protein Ribosomal protein s27-like protein


Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S1S4
#16: Protein Methyltransferase-like protein


Mass: 30362.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SC37
#17: Protein Pre-rRNA-processing protein PNO1


Mass: 28715.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S3T2
#18: Protein Serine/threonine-protein kinase RIO1


Mass: 59374.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)
References: UniProt: G0S3J5, non-specific serine/threonine protein kinase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#19: Protein Utp14


Mass: 104741.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S8Y4

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RNA chain , 1 types, 1 molecules A

#15: RNA chain pre-18S


Mass: 579124.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)

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Non-polymers , 3 types, 7 molecules

#20: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: pre-40S ribosome, state Tsr1-1* / Type: RIBOSOME / Entity ID: #1-#19 / Source: NATURAL
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
4RELIONCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstruction
CTF correctionDetails: Relion / Type: NONE
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6707 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6G18

6g18


Accession code: 6G18 / Source name: PDB / Type: experimental model

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