9HLZ image
Deposition Date 2024-12-06
Release Date 2025-12-17
Last Version Date 2026-03-04
Entry Detail
PDB ID:
9HLZ
Keywords:
RIBOSOME
Title:
Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae W303 (Taxon ID: 580240)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9HLZ validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RTC6
Chain IDs:LA (auth: 00)
Chain Length:93
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
UniProt ID:O14464 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):QRI5
Chain IDs:A (auth: 1)
Chain Length:111
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
UniProt ID:P32344 Pfam ID:PF08213
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):MRPL35
Chain IDs:MA (auth: 11)
Chain Length:367
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
UniProt ID:Q06678 Pfam ID:PF01161
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):FYV4
Chain IDs:B (auth: 2)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
UniProt ID:P38783 Pfam ID:PF09597
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):MRPL28
Chain IDs:NA (auth: 22)
Chain Length:147
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
UniProt ID:P36527 Pfam ID:PF09812
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RSM26
Chain IDs:C (auth: 3)
Chain Length:266
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
UniProt ID:P47141 Pfam ID:PF02777
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:OA (auth: 33)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:D (auth: 4)
Chain Length:321
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:PA (auth: 44)
Chain Length:140
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:E (auth: 5)
Chain Length:339
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:QA (auth: 55)
Chain Length:390
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:F (auth: 6)
Chain Length:345
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:RA (auth: 66)
Chain Length:281
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:G (auth: 7)
Chain Length:361
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:SA (auth: 77)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:H (auth: 8)
Chain Length:500
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:TA (auth: 88)
Chain Length:264
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:UA (auth: 99)
Chain Length:253
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:I (auth: A)
Chain Length:518
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polyribonucleotide
Molecule:21S mitochondrial rRNA
Chain IDs:VA (auth: AA)
Chain Length:3296
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:J (auth: B)
Chain Length:394
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:WA (auth: BB)
Chain Length:393
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:K (auth: C)
Chain Length:398
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:XA (auth: CC)
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:L (auth: D)
Chain Length:486
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:YA (auth: DD)
Chain Length:286
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:M (auth: E)
Chain Length:307
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:ZA (auth: EE)
Chain Length:292
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:N (auth: F)
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:AB (auth: FF)
Chain Length:214
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:O (auth: G)
Chain Length:247
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:BB (auth: GG)
Chain Length:139
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:P (auth: H)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:CB (auth: HH)
Chain Length:163
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:Q (auth: I)
Chain Length:278
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:DB (auth: II)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:R (auth: J)
Chain Length:203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:EB (auth: JJ)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:S (auth: K)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:FB (auth: KK)
Chain Length:232
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:T (auth: L)
Chain Length:153
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:GB (auth: LL)
Chain Length:238
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:U (auth: M)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:HB (auth: MM)
Chain Length:169
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:V (auth: N)
Chain Length:115
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:IB (auth: NN)
Chain Length:161
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:W (auth: O)
Chain Length:286
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:JB (auth: OO)
Chain Length:309
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:X (auth: P)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:KB (auth: PP)
Chain Length:263
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:Y (auth: Q)
Chain Length:237
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:LB (auth: QQ)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:Z (auth: R)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:MB (auth: RR)
Chain Length:371
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:AA (auth: S)
Chain Length:91
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:NB (auth: SS)
Chain Length:258
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:BA (auth: T)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:OB (auth: TT)
Chain Length:319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:CA (auth: U)
Chain Length:264
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:PB (auth: UU)
Chain Length:86
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:QB (auth: V)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:RB (auth: VV)
Chain Length:177
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:DA (auth: W)
Chain Length:450
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:SB (auth: WW)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:EA (auth: X)
Chain Length:110
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:TB (auth: XX)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:FA (auth: Y)
Chain Length:319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:UB (auth: YY)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:GA (auth: Z)
Chain Length:95
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:VB (auth: ZZ)
Chain Length:115
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:ATPase expression protein 1
Chain IDs:HA (auth: a)
Chain Length:518
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:WB (auth: aa)
Chain Length:3296
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:ATPase expression protein 2
Chain IDs:IA (auth: b)
Chain Length:394
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:XB (auth: bb)
Chain Length:393
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:ATPase synthesis protein 25,
Chain IDs:JA (auth: c)
Chain Length:398
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:YB (auth: cc)
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:ZB (auth: dd)
Chain Length:286
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polyribonucleotide
Molecule:15S mitochondrial rRNA
Chain IDs:AC (auth: r)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Polymer Type:polyribonucleotide
Molecule:E/E-site formyl-methionine tR
Chain IDs:KA (auth: t)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae W303
Ligand Molecules
GTP
MG
Primary Citation
Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation.
Nat.Struct.Mol.Biol. 33 245 258 (2026)
PMID: 41339860 DOI: 10.1038/s41594-025-01726-y

Abstact

Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In Saccharomyces cerevisiae, nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats using selective mitoribosome profiling and cryo-electron microscopy (cryo-EM) structural analysis. These analyses show that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicate that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to mitoribosomes stalled in the post-initiation, pre-elongation state revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5' untranslated region of the client mRNA and the mRNA channel exit to align the mRNA in the small subunit during initiation. Our findings provide a mechanistic basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position mitoribosomes at start codons.

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Protein

Chemical

Disease

Primary Citation of related structures
9HLZ
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