8D8K image
Deposition Date 2022-06-08
Release Date 2022-12-21
Last Version Date 2024-11-13
Entry Detail
PDB ID:
8D8K
Keywords:
Title:
Yeast mitochondrial small subunit assembly intermediate (State 2)
Biological Source:
Source Organism(s):
Method Details:
Experimental Method:
Resolution:
3.13 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:U (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 S26, mi
Gene (Uniprot):RSM26
Chain IDs:V (auth: 3)
Chain Length:266
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein MRP1, m
Gene (Uniprot):MRP1
Chain IDs:X (auth: 4)
Chain Length:321
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:AA (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 MRP51,
Gene (Uniprot):MRP51
Chain IDs:S (auth: A)
Chain Length:344
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein MRP4, m
Gene (Uniprot):MRP4
Chain IDs:T (auth: B)
Chain Length:394
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein VAR1, mitoc
Gene (Uniprot):VAR1
Chain IDs:C
Chain Length:94
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:W (auth: D)
Chain Length:486
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:Y (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:Z (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 S7, mit
Gene (Uniprot):RSM7
Chain IDs:BA (auth: G)
Chain Length:247
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:CA (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:37S ribosomal protein S9, mit
Gene (Uniprot):MRPS9
Chain IDs:DA (auth: I)
Chain Length:278
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S10, mi
Gene (Uniprot):RSM10
Chain IDs:FA (auth: J)
Chain Length:203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S18, mi
Gene (Uniprot):MRPS18
Chain IDs:GA (auth: K)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:MRPS12 isoform 1
Chain IDs:IA (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 SWS2, m
Gene (Uniprot):SWS2
Chain IDs:E (auth: M)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein MRP2, m
Gene (Uniprot):MRP2
Chain IDs:F (auth: N)
Chain Length:115
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:G (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:H (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:I (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:J (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 S19, mi
Gene (Uniprot):RSM19
Chain IDs:K (auth: S)
Chain Length:91
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein MRP21,
Gene (Uniprot):MRP21
Chain IDs:L (auth: T)
Chain Length:177
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S25, mi
Gene (Uniprot):RSM25
Chain IDs:M (auth: U)
Chain Length:264
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:N (auth: V)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S23, mi
Gene (Uniprot):RSM23
Chain IDs:O (auth: W)
Chain Length:450
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial 37S ribosomal p
Gene (Uniprot):RSM27
Chain IDs:P (auth: X)
Chain Length:110
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S24, mi
Gene (Uniprot):RSM24
Chain IDs:Q (auth: Y)
Chain Length:319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein MRP10,
Gene (Uniprot):MRP10
Chain IDs:R (auth: Z)
Chain Length:95
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:15S ribosomal RNA
Chain IDs:EA (auth: a)
Chain Length:344
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:unknown protein sequence
Chain IDs:HA (auth: c)
Chain Length:94
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:D (auth: d)
Chain Length:486
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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