8D8J image
Deposition Date 2022-06-08
Release Date 2022-12-21
Last Version Date 2024-06-12
Entry Detail
PDB ID:
8D8J
Keywords:
Title:
Yeast mitochondrial small subunit assembly intermediate (State 1)
Biological Source:
Source Organism(s):
Method Details:
Experimental Method:
Resolution:
3.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable S-adenosyl-L-methion
Gene (Uniprot):RSM22
Chain IDs:A (auth: 0)
Chain Length:628
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein FYV4, mitochondrial
Gene (Uniprot):FYV4
Chain IDs:I (auth: 2)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein MRP13,
Gene (Uniprot):MRP13
Chain IDs:B (auth: 5)
Chain Length:339
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S35, mi
Gene (Uniprot):MRPS35
Chain IDs:M (auth: 6)
Chain Length:345
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein NAM9, m
Gene (Uniprot):NAM9
Chain IDs:J (auth: D)
Chain Length:864
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S5, mit
Gene (Uniprot):MRPS5
Chain IDs:K (auth: E)
Chain Length:307
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein MRP17,
Gene (Uniprot):MRP17
Chain IDs:L (auth: F)
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S8, mit
Gene (Uniprot):MRPS8
Chain IDs:N (auth: H)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS12m
Chain IDs:P (auth: L)
Chain Length:153
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S28, mi
Gene (Uniprot):MRPS28
Chain IDs:D (auth: O)
Chain Length:286
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S16, mi
Gene (Uniprot):MRPS16
Chain IDs:E (auth: P)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S17, mi
Gene (Uniprot):MRPS17
Chain IDs:F (auth: Q)
Chain Length:237
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein RSM18,
Gene (Uniprot):RSM18
Chain IDs:G (auth: R)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein PET123,
Gene (Uniprot):PET123
Chain IDs:H (auth: V)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:15S ribosomal RNA
Chain IDs:O (auth: a)
Chain Length:1713
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial group I intron
Chain IDs:C (auth: d)
Chain Length:864
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Primary Citation
Principles of mitoribosomal small subunit assembly in eukaryotes.
Nature 614 175 181 (2023)
PMID: 36482135 DOI: 10.1038/s41586-022-05621-0

Abstact

Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism1. Here we used cryo-electron microscopy to determine nine structures of native yeast and human mitoribosomal small subunit assembly intermediates, illuminating the mechanistic basis for how GTPases are used to control early steps of decoding centre formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins have active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins and rRNA that are required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies.

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