9XAH | pdb_00009xah

Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum, state B1*


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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: 4,473.28 kDa 
  • Atom Count: 228,132 
  • Modeled Residue Count: 26,168 
  • Deposited Residue Count: 35,078 
  • Unique protein chains: 59
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2-like proteinA [auth UA]904Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14B [auth UB]907Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Sas10 C-terminal domain-containing proteinC [auth UC]648Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
UTP4D [auth UD]884Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
U3 snoRNP proteinE [auth UF]414Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
U three protein 7F [auth UG]558Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10G [auth UJ]1,802Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11H [auth UK]270Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Small-subunit processome Utp12 domain-containing proteinI [auth UL]962Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13 C-terminal domain-containing proteinJ [auth UM]912Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
UTP14K [auth UN]633Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15 C-terminal domain-containing proteinL [auth UO]557Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
UTP17M [auth UQ]960Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
UTP18N [auth UR]618Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative U3 snoRNP proteinO [auth UU]1,049Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
UTP24P [auth UX]193Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein C8F11.04Q [auth UZ]391Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinR [auth CA],
S [auth CB]
313Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleolar protein 56T [auth CC]523Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleolar protein 58U [auth CD]582Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 2V [auth CE],
W [auth CF]
127Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing proteinX [auth CG]630Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinY [auth CH]411Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Bms1-type G domain-containing proteinZ [auth CI]1,163Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S445 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3AA [auth CJ]183Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4BA [auth CK]297Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
mpp10CA [auth CL]720Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 13DA [auth CM]446Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleolar essential protein 1EA [auth CN],
FA [auth CO]
252Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentGA [auth CP]322Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1HA [auth CQ]259Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA cytidine acetyltransferaseIA [auth CR],
JA [auth CS]
1,073Thermochaetoides thermophilaMutation(s): 0 
EC: 2.3.1
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Fcf2 pre-rRNA processing C-terminal domain-containing proteinKA [auth CT]203Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1LA [auth Ca]255Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4MA [auth Cb]264Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s5-like proteinNA [auth Cc]212Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6OA [auth Cd]239Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7PA [auth Ce]203Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8QA [auth Cf]202Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinRA [auth Cg]190Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13-like proteinSA [auth Ch]151Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinTA [auth Ci]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: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-like proteinUA [auth Cj]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: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinVA [auth Ck]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: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-like proteinWA [auth Cm]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: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein s23-like proteinXA [auth Cn]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: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24YA [auth Co]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: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-like proteinZA [auth Cp]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: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Faf1AB [auth CU]311Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S5F1 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ENP2DB [auth CW]668Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S902 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
UTP20EB [auth UT]2,612Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SHP3 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
UTP8FB [auth UH]930Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for P0CT47 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
Small-subunit processome Utp12 domain-containing proteinGB [auth UE],
MB [auth UI]
410Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RYX2 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
CCAAT-binding factor domain-containing proteinHB [auth US]549Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RZL4 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal proteinIB [auth Cl]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: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
Bystin-like proteinJB [auth CX]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: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein lcp5-like proteinKB [auth CY]381Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S7Z2 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BFR2LB [auth CZ]609Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SAJ6 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
UTP16NB [auth UP]364Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S612 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719))
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Entity ID: 50
MoleculeChains LengthOrganismImage
35s rnaBB [auth C1]2,344Thermochaetoides thermophila
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Entity ID: 51
MoleculeChains LengthOrganismImage
u3 rnaCB [auth C2]274Thermochaetoides thermophila
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

Currently 9XAH does not have a validation slider image.



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