EMD-3847

Single-particle
3.2 Å
EMD-3847
3D View Gallery
Deposition: 12/08/2017
Map released: 11/10/2017
Last modified: 25/11/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-3847
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EMICSS annotations (xml)

Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum

EMD-3847

Single-particle
3.2 Å
EMD-3847
3D View Gallery
Deposition: 12/08/2017
Map released: 11/10/2017
Last modified: 25/11/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Name: The 90S Pre-ribosomne
Complex [1]
Name: The 90S Pre-ribosomne
Natural source [1]
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Protein [49]
LEVO
Name: Periodic tryptophan protein 2-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
ribosome biogenesis rRNA processing

Cellular location:
nucleolus
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 100 kDa -
LEVO
Name: Utp2
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 103 kDa -
LEVO
Name: Utp3
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 73 kDa -
LEVO
Name: Utp4
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 97 kDa -
LEVO
Name: Utp6
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 46 kDa -
LEVO
Name: Utp7
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 63 kDa -
LEVO
Name: Utp10
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 198 kDa -
LEVO
Name: U3 small nucleolar RNA-associated protein 11
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
rRNA processing

Cellular location:
nucleolus small-subunit processome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 31 kDa -
LEVO
Name: Utp12
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
ribosome biogenesis rRNA processing

Cellular location:
nucleolus
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 107 kDa -
LEVO
Name: Utp13
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
rRNA processing

Cellular location:
small-subunit processome nucleolus
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 100 kDa -
LEVO
Name: Utp14
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [1]


Cellular location:
nucleolus
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 104 kDa -
LEVO
Name: Utp15
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 60 kDa -
LEVO
Name: Utp17
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 105 kDa -
LEVO
Name: Utp18
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 69 kDa -
LEVO
Name: Putative U3 snoRNP protein
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [2]
Biological process:
rRNA processing

Cellular location:
small-subunit processome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 115 kDa -
LEVO
Name: Utp24
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 22 kDa -
LEVO
Name: Utp30
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 43 kDa -
LEVO
Name: Nop1
Number of copies: 2
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 32 kDa -
LEVO
Name: Putative nucleolar protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 57 kDa -
LEVO
Name: Nop58
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 64 kDa -
LEVO
Name: Snu13
Number of copies: 2
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 13 kDa -
LEVO
Name: Rrp9
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 69 kDa -
LEVO
Name: RNA 3'-terminal phosphate cyclase-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
RNA processing ribosome biogenesis
Molecular function:
catalytic activity
Cellular location:
nucleolus
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 43 kDa -
LEVO
Name: Bms1
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [11]
Biological process:
ribosome biogenesis regulation of rRNA processing endonucleolytic cleavage in 5'-ETS 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)
Molecular function:
U3 snoRNA binding GTP binding GTPase activity
Cellular location:
cytoplasm small-subunit processome 90S preribosome nucleolus
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 134 kDa -
LEVO
Name: Imp3
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 21 kDa -
LEVO
Name: Putative U3 small nucleolar ribonucleoprotein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 34 kDa -
LEVO
Name: Putative U3 small nucleolar ribonucleoprotein protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
rRNA processing

Cellular location:
Mpp10 complex sno(s)RNA-containing ribonucleoprotein complex
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 86 kDa -
LEVO
Name: Sof1
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 50 kDa -
LEVO
Name: Emg1
Number of copies: 2
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 27 kDa -
LEVO
Name: KRR1 small subunit processome component
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
rRNA processing endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Molecular function:
RNA binding
Cellular location:
ribonucleoprotein complex small-subunit processome preribosome, small subunit precursor nucleolus
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 37 kDa -
LEVO
Name: Pre-rRNA-processing protein PNO1
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
ribosome biogenesis
Molecular function:
RNA binding
Cellular location:
nucleolus cytoplasm
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 28 kDa -
LEVO
Name: RNA cytidine acetyltransferase
EC number: 2.3.1.-
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [12]
Biological process:
mRNA modification tRNA acetylation rRNA modification ribosomal small subunit biogenesis
Molecular function:
N-acetyltransferase activity snoRNA binding rRNA cytidine N-acetyltransferase activity tRNA binding ATP binding
Cellular location:
nucleolus preribosome, small subunit precursor small-subunit processome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 119 kDa -
LEVO
Name: Fcf2
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [2]


Cellular location:
nucleolus nucleus
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 22 kDa -
LEVO
Name: 40S ribosomal protein S1
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
cytosolic small ribosomal subunit
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 29 kDa -
LEVO
Name: 40S ribosomal protein S4
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
translation
Molecular function:
rRNA binding structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 29 kDa -
LEVO
Name: 40S ribosomal protein s5-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
rRNA export from nucleus translation
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
small ribosomal subunit cytosolic small ribosomal subunit
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 23 kDa -
LEVO
Name: 40S ribosomal protein S6
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex cytoplasm ribosome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 27 kDa -
LEVO
Name: 40S ribosomal protein S7-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 23 kDa -
LEVO
Name: 40S ribosomal protein S8
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 23 kDa -
LEVO
Name: 40S ribosomal protein s9-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
rRNA binding structural constituent of ribosome
Cellular location:
small ribosomal subunit
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 22 kDa -
LEVO
Name: 40S ribosomal protein S13-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) translation
Molecular function:
small ribosomal subunit rRNA binding structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome cytosolic small ribosomal subunit
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 16 kDa -
LEVO
Name: 40S ribosomal protein S14-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome cytoplasm
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 16 kDa -
LEVO
Name: 40S ribosomal protein S16-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex cytoplasm ribosome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 15 kDa -
LEVO
Name: 40S ribosomal protein S11-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 18 kDa -
LEVO
Name: 40S ribosomal protein S22-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 14 kDa -
LEVO
Name: 40S ribosomal protein s23-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
small ribosomal subunit
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 15 kDa -
LEVO
Name: 40S ribosomal protein S24
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
methylation translation
Molecular function:
methyltransferase activity structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome cytoplasm
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 15 kDa -
LEVO
Name: 40S ribosomal protein S28-like protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 7 kDa -
LEVO
Name: Faf1
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 34 kDa -
RNA [2]
Name: 35S rRNA
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 827 kDa -
Name: U3 snoRNA
Number of copies: 1
Natural source
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecular weight
Experimental Theoretical Method
- 87 kDa -
Ligand [1]
Name: ZINC ION
HET code: ZN
Number of copies: 1
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 65 Da -