EMD-0372

Single-particle
3.5 Å
EMD-0372
3D View Gallery
Deposition: 29/11/2018
Map released: 13/03/2019
Last modified: 08/01/2020
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-0372
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EMICSS annotations (xml)

Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit

EMD-0372

Single-particle
3.5 Å
EMD-0372
3D View Gallery
Deposition: 29/11/2018
Map released: 13/03/2019
Last modified: 08/01/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Name: Pre-Lsg1 (PL) pre-60S ribosomal subunit
Complex [1]
Name: Pre-Lsg1 (PL) pre-60S ribosomal subunit
Natural source [1]
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
RNA [3]
Name: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
Number of copies: 1
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 1 MDa -
Name: 5S rRNA
Number of copies: 1
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 38 kDa -
Name: 5.8S RNA
Number of copies: 1
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 50 kDa -
Protein [44]
LEVO
Name: Tyrosine-protein phosphatase YVH1
EC number: 3.1.3.48
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [13]
Biological process:
dephosphorylation positive regulation of autophagosome assembly ascospore wall assembly protein dephosphorylation ribosomal large subunit assembly ribosomal large subunit export from nucleus meiotic cell cycle
Molecular function:
protein tyrosine phosphatase activity preribosome binding protein tyrosine/serine/threonine phosphatase activity
Cellular location:
cytoplasm cytoplasmic stress granule nucleus
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 41 kDa -
LEVO
Name: 60S ribosomal protein L2-A
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome rRNA binding RNA binding
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 27 kDa -
LEVO
Name: 60S ribosomal protein L3
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [10]
Biological process:
translation cytoplasmic translation rRNA processing ribosomal large subunit assembly maintenance of translational fidelity
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
cytoplasm cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 43 kDa -
LEVO
Name: 60S ribosomal protein L4-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
cytoplasmic translation
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
cytosol nucleus cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 39 kDa -
LEVO
Name: 60S ribosomal protein L5
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
ribosomal large subunit assembly cytoplasmic translation
Molecular function:
5S rRNA binding structural constituent of ribosome
Cellular location:
cytoplasm cytosol cytosolic large ribosomal subunit nucleus
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 33 kDa -
LEVO
Name: 60S ribosomal protein L6-A
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
ribosomal large subunit assembly cytoplasmic translation
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 20 kDa -
LEVO
Name: 60S ribosomal protein L7-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [9]
Biological process:
maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cytoplasmic translation maturation of LSU-rRNA ribosomal large subunit biogenesis
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
cytosolic large ribosomal subunit cytosol cytoplasm
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 27 kDa -
LEVO
Name: 60S ribosomal protein L8-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
cytoplasmic translation maturation of LSU-rRNA
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 28 kDa -
LEVO
Name: 60S ribosomal protein L9-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome rRNA binding
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 21 kDa -
LEVO
Name: 60S ribosomal protein L11-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
cytoplasmic translation ribosomal large subunit assembly
Molecular function:
rRNA binding RNA binding structural constituent of ribosome
Cellular location:
cytosol nucleus cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 19 kDa -
LEVO
Name: 60S ribosomal protein L13-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 22 kDa -
LEVO
Name: 60S ribosomal protein L14-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
macroautophagy ribosomal large subunit biogenesis cytoplasmic translation
Molecular function:
structural constituent of ribosome RNA binding
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 15 kDa -
LEVO
Name: 60S ribosomal protein L42-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
cytoplasmic translation response to cycloheximide response to antibiotic
Molecular function:
structural constituent of ribosome
Cellular location:
cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 12 kDa -
LEVO
Name: 60S ribosomal protein L43-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 10 kDa -
LEVO
Name: Ribosomal Protein uL1
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 18 kDa -
LEVO
Name: 60S ribosomal protein L15-A
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome RNA binding
Cellular location:
cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 24 kDa -
LEVO
Name: 60S ribosomal protein L16-A
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
cytoplasmic translation negative regulation of translation
Molecular function:
RNA binding mRNA binding structural constituent of ribosome
Cellular location:
cytosol cytosolic large ribosomal subunit ribosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 22 kDa -
LEVO
Name: 60S ribosomal protein L17-A
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cytoplasmic translation
Molecular function:
structural constituent of ribosome
Cellular location:
cytosolic large ribosomal subunit cytosol preribosome, large subunit precursor cytoplasm
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 20 kDa -
LEVO
Name: 60S ribosomal protein L18-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome RNA binding
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 20 kDa -
LEVO
Name: 60S ribosomal protein L19-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
cytoplasmic translation
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 21 kDa -
LEVO
Name: 60S ribosomal protein L20-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome
Cellular location:
cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 20 kDa -
LEVO
Name: 60S ribosomal protein L21-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 18 kDa -
LEVO
Name: 60S ribosomal protein L22-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome RNA binding
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 13 kDa -
LEVO
Name: 60S ribosomal protein L23-A
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome large ribosomal subunit rRNA binding
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 14 kDa -
LEVO
Name: 60S ribosomal protein L24-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome RNA binding mRNA binding
Cellular location:
cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 17 kDa -
LEVO
Name: 60S ribosomal protein L25
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
ribosomal large subunit assembly cytoplasmic translation
Molecular function:
rRNA binding RNA binding structural constituent of ribosome
Cellular location:
preribosome, large subunit precursor cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 15 kDa -
LEVO
Name: 60S ribosomal protein L26-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
cytoplasmic translation ribosomal large subunit biogenesis
Molecular function:
structural constituent of ribosome RNA binding
Cellular location:
cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 14 kDa -
LEVO
Name: 60S ribosomal protein L27-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome
Cellular location:
cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 15 kDa -
LEVO
Name: 60S ribosomal protein L28
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome RNA binding
Cellular location:
cytoplasm cytosolic large ribosomal subunit nucleus cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 16 kDa -
LEVO
Name: 60S ribosomal protein L29
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 6 kDa -
LEVO
Name: 60S ribosomal protein L30
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [9]
Biological process:
rRNA processing negative regulation of mRNA splicing, via spliceosome cytoplasmic translation
Molecular function:
pre-mRNA 5'-splice site binding RNA binding structural constituent of ribosome
Cellular location:
cytoplasm cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 11 kDa -
LEVO
Name: 60S ribosomal protein L31-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
regulation of translational fidelity cytoplasmic translation
Molecular function:
structural constituent of ribosome
Cellular location:
cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 12 kDa -
LEVO
Name: 60S ribosomal protein L32
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 14 kDa -
LEVO
Name: 60S ribosomal protein L33-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
ribosomal large subunit biogenesis cytoplasmic translation
Molecular function:
structural constituent of ribosome
Cellular location:
cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 12 kDa -
LEVO
Name: 60S ribosomal protein L34-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 13 kDa -
LEVO
Name: 60S ribosomal protein L35-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
cytoplasmic translation maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Molecular function:
structural constituent of ribosome mRNA binding
Cellular location:
preribosome, large subunit precursor cytosolic large ribosomal subunit cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 13 kDa -
LEVO
Name: 60S ribosomal protein L36-A
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
cytoplasmic translation
Molecular function:
structural constituent of ribosome RNA binding
Cellular location:
cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 11 kDa -
LEVO
Name: 60S ribosomal protein L37-A
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [9]
Biological process:
cytoplasmic translation cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Molecular function:
RNA binding metal ion binding structural constituent of ribosome rRNA binding
Cellular location:
cytosol cytosolic large ribosomal subunit preribosome, large subunit precursor
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 9 kDa -
LEVO
Name: 60S ribosomal protein L38
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
protein-RNA complex assembly ribonucleoprotein complex assembly cytoplasmic translation
Molecular function:
structural constituent of ribosome
Cellular location:
cytoplasm cytosol cytosolic large ribosomal subunit
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 8 kDa -
LEVO
Name: 60S ribosomal protein L39
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 6 kDa -
LEVO
Name: Ubiquitin-60S ribosomal protein L40
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [14]
Biological process:
protein ubiquitination ribosomal large subunit export from nucleus ribosome biogenesis ribosomal large subunit assembly modification-dependent protein catabolic process cytoplasmic translation
Molecular function:
protein tag activity structural constituent of ribosome protein tag ubiquitin protein ligase binding
Cellular location:
cytosolic large ribosomal subunit cytoplasm cytosol nucleus
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 14 kDa -
LEVO
Name: 60S ribosomal export protein NMD3
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
protein transport ribosomal large subunit export from nucleus
Molecular function:
large ribosomal subunit rRNA binding ribosomal large subunit binding
Cellular location:
nucleus nucleoplasm cytoplasm cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 59 kDa -
LEVO
Name: Ribosomal protein L12
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 15 kDa -
LEVO
Name: Eukaryotic translation initiation factor 6
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [18]
Biological process:
cytosolic ribosome assembly maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) assembly of large subunit precursor of preribosome ribosomal subunit export from nucleus maturation of LSU-rRNA maturation of 5.8S rRNA rRNA processing mature ribosome assembly maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ribosomal large subunit biogenesis
Molecular function:
ribosome binding ribosomal large subunit binding translation initiation factor activity
Cellular location:
preribosome, large subunit precursor cytosol nucleus nucleolus cytoplasm
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 26 kDa -