9AXU image
Deposition Date 2024-03-06
Release Date 2024-10-16
Last Version Date 2024-11-20
Entry Detail
PDB ID:
9AXU
Keywords:
Title:
Non-translating S. pombe ribosome large subunit
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.94 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL42
Gene (Uniprot):rpl42
Chain IDs:A (auth: 0)
Chain Length:106
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL43A
Gene (Uniprot):rpl4301
Chain IDs:B (auth: 1)
Chain Length:94
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:C (auth: 2)
Chain Length:3498
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:D (auth: 3)
Chain Length:246
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:E (auth: 4)
Chain Length:165
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2C
Gene (Uniprot):rpl803
Chain IDs:F (auth: N)
Chain Length:253
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3A
Gene (Uniprot):rpl301
Chain IDs:G (auth: O)
Chain Length:109
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4A
Gene (Uniprot):rpl402
Chain IDs:H (auth: P)
Chain Length:363
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18B
Gene (Uniprot):rpl502
Chain IDs:I (auth: Q)
Chain Length:294
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL6
Gene (Uniprot):rpl6
Chain IDs:J (auth: R)
Chain Length:195
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30C
Gene (Uniprot):rpl701
Chain IDs:K (auth: S)
Chain Length:251
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL8
Gene (Uniprot):rpl8
Chain IDs:L (auth: T)
Chain Length:122
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6B
Gene (Uniprot):rpl902
Chain IDs:M (auth: U)
Chain Length:189
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16A
Gene (Uniprot):rpl1001
Chain IDs:N (auth: V)
Chain Length:221
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5A
Gene (Uniprot):rpl1101
Chain IDs:O (auth: W)
Chain Length:174
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL13
Gene (Uniprot):rpl13
Chain IDs:P (auth: X)
Chain Length:208
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL14
Gene (Uniprot):rpl14
Chain IDs:Q (auth: Y)
Chain Length:134
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL15B
Gene (Uniprot):rpl1502
Chain IDs:R (auth: Z)
Chain Length:201
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13A
Gene (Uniprot):rpl1602
Chain IDs:S (auth: a)
Chain Length:197
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22A
Gene (Uniprot):rpl1701
Chain IDs:T (auth: b)
Chain Length:187
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL18B
Gene (Uniprot):rpl1802
Chain IDs:U (auth: c)
Chain Length:187
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL19B
Gene (Uniprot):rpl1902
Chain IDs:V (auth: d)
Chain Length:193
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL20A
Gene (Uniprot):rpl2001
Chain IDs:W (auth: e)
Chain Length:176
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL21B
Gene (Uniprot):rpl2102
Chain IDs:X (auth: f)
Chain Length:160
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL22
Gene (Uniprot):rpl22
Chain IDs:Y (auth: g)
Chain Length:117
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14B
Gene (Uniprot):rpl2302
Chain IDs:Z (auth: h)
Chain Length:139
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL24B
Gene (Uniprot):rpl2402
Chain IDs:AA (auth: i)
Chain Length:149
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23A
Gene (Uniprot):rpl2501
Chain IDs:BA (auth: j)
Chain Length:141
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rpl26
Chain IDs:CA (auth: k)
Chain Length:126
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL27A
Gene (Uniprot):rpl2701
Chain IDs:DA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15B
Gene (Uniprot):rpl2801
Chain IDs:EA (auth: m)
Chain Length:148
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL29
Gene (Uniprot):rpl29
Chain IDs:FA (auth: n)
Chain Length:253
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL30A
Gene (Uniprot):rpl3001
Chain IDs:GA (auth: o)
Chain Length:109
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL31
Gene (Uniprot):rpl31
Chain IDs:HA (auth: p)
Chain Length:363
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL32A
Gene (Uniprot):rpl3202
Chain IDs:IA (auth: q)
Chain Length:294
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL33A
Gene (Uniprot):rpl35b
Chain IDs:JA (auth: r)
Chain Length:195
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL34B
Gene (Uniprot):rpl3402
Chain IDs:KA (auth: s)
Chain Length:251
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpl35
Chain IDs:LA (auth: t)
Chain Length:122
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL36B
Gene (Uniprot):rpl3602
Chain IDs:MA (auth: u)
Chain Length:189
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL37B
Gene (Uniprot):rpl3702
Chain IDs:NA (auth: v)
Chain Length:221
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL38A
Gene (Uniprot):rpl3801
Chain IDs:OA (auth: w)
Chain Length:174
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL39
Gene (Uniprot):rpl39
Chain IDs:PA (auth: x)
Chain Length:208
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL28
Gene (Uniprot):rpl44
Chain IDs:QA (auth: y)
Chain Length:134
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Primary Citation
Ribosomes hibernate on mitochondria during cellular stress.
Nat Commun 15 8666 8666 (2024)
PMID: 39379376 DOI: 10.1038/s41467-024-52911-4

Abstact

Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence.

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