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Yorodumi- EMDB-66677: Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 WT) from Ch... -
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Basic information
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| Title | Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 WT) from Chaetomium thermophilum, state A | |||||||||
Map data | local resolution filtered map using Relion | |||||||||
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Keywords | 90S pre-ribosome / Rrp12 / Enp1 / ribosome biogenesis / RIBOSOME | |||||||||
| Function / homology | Function and homology informationbox H/ACA snoRNP complex / snRNA pseudouridine synthesis / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / Mpp10 complex ...box H/ACA snoRNP complex / snRNA pseudouridine synthesis / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / snoRNA guided rRNA 2'-O-methylation / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D methylation guide snoRNP complex / positive regulation of rRNA processing / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / rRNA base methylation / U3 snoRNA binding / snoRNA binding / preribosome, small subunit precursor / positive regulation of transcription by RNA polymerase I / 90S preribosome / RNA processing / RNA endonuclease activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA splicing / methyltransferase activity / spliceosomal complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / mRNA splicing, via spliceosome / small-subunit processome / mRNA processing / rRNA processing / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / methylation / nuclear membrane / tRNA binding / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / GTPase activity / GTP binding / nucleolus / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | Thermochaetoides thermophila (fungus) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Lau B / Li Y / Zhu J / Fischer P / Hong X / Yuan R / Beckmann R / Hurt E / Cheng J | |||||||||
| Funding support | 1 items
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Citation | Journal: Cell Rep / Year: 2026Title: 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 |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_66677.map.gz | 235.4 MB | EMDB map data format | |
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| Header (meta data) | emd-66677-v30.xml emd-66677.xml | 94.7 KB 94.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_66677_fsc.xml | 16.9 KB | Display | FSC data file |
| Images | emd_66677.png | 133.5 KB | ||
| Filedesc metadata | emd-66677.cif.gz | 25.3 KB | ||
| Others | emd_66677_additional_1.map.gz emd_66677_additional_2.map.gz emd_66677_half_map_1.map.gz emd_66677_half_map_2.map.gz | 338.1 MB 365.1 MB 338.2 MB 338.2 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-66677 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-66677 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9xa7MC ![]() 9xa8C ![]() 9xa9C ![]() 9xaaC ![]() 9xabC ![]() 9xacC ![]() 9xadC ![]() 9xaeC ![]() 9xafC ![]() 9xagC ![]() 9xahC ![]() 9xaiC ![]() 9xajC ![]() 9xakC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_66677.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | local resolution filtered map using Relion | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.146 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: consensus refined map without post processing
| File | emd_66677_additional_1.map | ||||||||||||
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| Annotation | consensus refined map without post processing | ||||||||||||
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-Additional map: local resolution filtered map using deepEMhancer
| File | emd_66677_additional_2.map | ||||||||||||
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| Annotation | local resolution filtered map using deepEMhancer | ||||||||||||
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-Half map: #2
| File | emd_66677_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_66677_half_map_2.map | ||||||||||||
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Sample components
+Entire : 90S pre-ribosome, state A
+Supramolecule #1: 90S pre-ribosome, state A
+Macromolecule #1: Periodic tryptophan protein 2-like protein
+Macromolecule #2: Nucleolar complex protein 14
+Macromolecule #3: Sas10 C-terminal domain-containing protein
+Macromolecule #4: UTP4
+Macromolecule #5: U3 snoRNP protein
+Macromolecule #6: U three protein 7
+Macromolecule #7: U3 small nucleolar RNA-associated protein 10
+Macromolecule #8: U3 small nucleolar RNA-associated protein 11
+Macromolecule #9: Small-subunit processome Utp12 domain-containing protein
+Macromolecule #10: U3 small nucleolar RNA-associated protein 13 C-terminal domain-co...
+Macromolecule #11: UTP14
+Macromolecule #12: U3 small nucleolar RNA-associated protein 15 C-terminal domain-co...
+Macromolecule #13: UTP17
+Macromolecule #14: UTP18
+Macromolecule #15: Putative U3 snoRNP protein
+Macromolecule #16: UTP24
+Macromolecule #17: Ribosome biogenesis protein C8F11.04
+Macromolecule #18: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #19: Nucleolar protein 56
+Macromolecule #20: Nucleolar protein 58
+Macromolecule #21: H/ACA ribonucleoprotein complex subunit 2
+Macromolecule #22: Ribosomal RNA-processing protein
+Macromolecule #23: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #24: Bms1-type G domain-containing protein
+Macromolecule #25: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #26: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #27: Putative U3 small nucleolar ribonucleoprotein protein
+Macromolecule #28: DDB1- and CUL4-associated factor 13
+Macromolecule #29: Nucleolar essential protein 1
+Macromolecule #30: KRR1 small subunit processome component
+Macromolecule #31: Pre-rRNA-processing protein PNO1
+Macromolecule #32: RNA cytidine acetyltransferase
+Macromolecule #33: Fcf2 pre-rRNA processing C-terminal domain-containing protein
+Macromolecule #34: Small ribosomal subunit protein eS1
+Macromolecule #35: 40S ribosomal protein s5-like protein
+Macromolecule #36: 40S ribosomal protein S7
+Macromolecule #37: 40S ribosomal protein s9-like protein
+Macromolecule #38: 40S ribosomal protein S13-like protein
+Macromolecule #39: 40S ribosomal protein S14-like protein
+Macromolecule #40: 40S ribosomal protein S16-like protein
+Macromolecule #41: 40S ribosomal protein S22-like protein
+Macromolecule #42: 40S ribosomal protein s23-like protein
+Macromolecule #43: Small ribosomal subunit protein eS24
+Macromolecule #44: 40S ribosomal protein S28-like protein
+Macromolecule #45: Faf1
+Macromolecule #48: UTP8
+Macromolecule #49: Small-subunit processome Utp12 domain-containing protein
+Macromolecule #50: CCAAT-binding factor domain-containing protein
+Macromolecule #51: Putative ribosomal protein
+Macromolecule #52: Bystin-like protein
+Macromolecule #53: U3 small nucleolar ribonucleoprotein protein lcp5-like protein
+Macromolecule #54: UTP16
+Macromolecule #46: 35S rRNA
+Macromolecule #47: U3 snoRNA
+Macromolecule #55: ZINC ION
+Macromolecule #56: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.4 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination 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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About Yorodumi



Keywords
Thermochaetoides thermophila (fungus)
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Processing
FIELD EMISSION GUN


