9HLZ image
Deposition Date 2024-12-06
Release Date 2025-12-17
Last Version Date 2025-12-17
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 protein bL36m
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 protein mS38
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 protein mL38
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 protein mS41
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 protein mL40
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 protein mS42
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 protein mL41
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 protein mS43
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 protein mL43
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 protein mS44
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 protein mL44
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 protein mS45
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 protein mL46
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 protein mS46
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 protein mL49
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 protein mS47
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 protein mL50
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 protein mL57
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 protein bS1m
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 protein uS2m
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 protein uL2m
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 protein uS3m
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 protein uL3m
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 protein uS4m
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 protein uL4m
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 protein uS5m
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 protein uL5m
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 protein bS6m
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 protein uL6m
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 protein uS7m
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 protein bL9m
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 protein uS8m
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 protein uL13m
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 protein uS9m
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 protein uL14m
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 protein uS10m
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 protein uL15m
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 protein uS11m
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 protein uL16m
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 protein uS12m
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 protein bL17m
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 protein uS13m
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 protein bL19m
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 protein uS14m
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 protein bL21m
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 protein uS15m
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 protein uL22m
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 protein bS16m
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 protein uL23m
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 protein uS17m
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 protein uL24m
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 protein bS18m
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 protein bL27m
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 protein uS19m
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 protein bL28m
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 protein bS21m
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 protein uL29m
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 protein mS23
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 protein uL30m
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 protein mS26
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 protein bL31m
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 protein mS29
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 protein bL32m
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 protein mS33
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 protein bL33m
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 protein mS35
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 protein bL34m
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 protein mS37
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 protein bL35m
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 protein mL58
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 protein mL59
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, mitochondrial
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 protein mL60
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 protein mL67
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 tRNA
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. ? ? ? (2025)
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
9HLZ
Feedback Form
Name
Email
Institute
Feedback