7NQL image
Entry Detail
PDB ID:
7NQL
EMDB ID:
Keywords:
Title:
55S mammalian mitochondrial ribosome with ICT1 and P site tRNAMet
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2021-03-01
Release Date:
2021-05-05
Method Details:
Experimental Method:
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:12S rRNA
Chain IDs:UA (auth: AA)
Chain Length:382
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S2
Chain IDs:YA (auth: AB)
Chain Length:289
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S24
Chain IDs:ZA (auth: AC)
Chain Length:167
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S5
Chain IDs:AB (auth: AE)
Chain Length:455
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:bS6m
Chain IDs:BB (auth: AF)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S7
Chain IDs:CB (auth: AG)
Chain Length:410
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uS9m
Chain IDs:DB (auth: AI)
Chain Length:106
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S10
Chain IDs:EB (auth: AJ)
Chain Length:200
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uS11m
Chain IDs:FB (auth: AK)
Chain Length:196
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S12
Chain IDs:GB (auth: AL)
Chain Length:139
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S14
Chain IDs:HB (auth: AN)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uS15m
Chain IDs:IB (auth: AO)
Chain Length:239
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S16, mitochondrial
Chain IDs:JB (auth: AP)
Chain Length:258
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uS17m
Chain IDs:KB (auth: AQ)
Chain Length:130
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S18C
Chain IDs:MB (auth: AR)
Chain Length:143
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:bS21m
Chain IDs:NB (auth: AU)
Chain Length:87
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polyribonucleotide
Description:fMet-tRNAMet (P site)
Chain IDs:OB (auth: AV)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:PB (auth: AX)
Chain Length:6
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:unknown
Chain IDs:QB (auth: AZ)
Chain Length:18
Number of Molecules:1
Biological Source:unidentified
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S22
Chain IDs:RB (auth: Aa)
Chain Length:382
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mS23
Chain IDs:SB (auth: Ab)
Chain Length:289
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S25
Chain IDs:TB (auth: Ac)
Chain Length:167
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S26
Chain IDs:UB (auth: Ad)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S27
Chain IDs:VB (auth: Ae)
Chain Length:455
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitoribosomal protein ms28, mrps28
Chain IDs:WB (auth: Af)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Death associated protein 3
Chain IDs:XB (auth: Ag)
Chain Length:410
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S31
Chain IDs:YB (auth: Ah)
Chain Length:387
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mS33
Chain IDs:ZB (auth: Ai)
Chain Length:106
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mS34
Chain IDs:AC (auth: Aj)
Chain Length:200
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S35
Chain IDs:BC (auth: Ak)
Chain Length:196
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mS37
Chain IDs:CC (auth: Am)
Chain Length:118
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Aurora kinase A interacting protein 1
Chain IDs:DC (auth: An)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Pentatricopeptide repeat domain 3
Chain IDs:EC (auth: Ao)
Chain Length:239
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S18b, mitochondrial
Chain IDs:FC (auth: Ap)
Chain Length:258
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L27
Chain IDs:IC (auth: B0)
Chain Length:148
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L28
Chain IDs:JC (auth: B1)
Chain Length:256
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L47
Chain IDs:KC (auth: B2)
Chain Length:252
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uL30m
Chain IDs:LC (auth: B3)
Chain Length:161
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:bL31m
Chain IDs:MC (auth: B4)
Chain Length:126
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:bL32m
Chain IDs:NC (auth: B5)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:bL33m
Chain IDs:OC (auth: B6)
Chain Length:65
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L34
Chain IDs:A (auth: B7)
Chain Length:95
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L35
Chain IDs:B (auth: B8)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Ribosomal protein
Chain IDs:C (auth: B9)
Chain Length:100
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:D (auth: BA)
Chain Length:1571
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polyribonucleotide
Description:CP tRNAPhe
Chain IDs:E (auth: BB)
Chain Length:73
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uL2m
Chain IDs:F (auth: BD)
Chain Length:206
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:ICT1
Chain IDs:G (auth: BE)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L4
Chain IDs:H (auth: BF)
Chain Length:294
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L9
Chain IDs:I (auth: BI)
Chain Length:268
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L10
Chain IDs:J (auth: BJ)
Chain Length:262
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L11
Chain IDs:K (auth: BK)
Chain Length:269
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Chain IDs:L (auth: BL)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:uL13m
Chain IDs:M (auth: BN)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uL14m
Chain IDs:N (auth: BO)
Chain Length:145
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uL15m
Chain IDs:O (auth: BP)
Chain Length:112
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uL16m
Chain IDs:P (auth: BQ)
Chain Length:138
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:bL17m
Chain IDs:Q (auth: BR)
Chain Length:169
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L18
Chain IDs:R (auth: BS)
Chain Length:180
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L19
Chain IDs:S (auth: BT)
Chain Length:292
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L20
Chain IDs:T (auth: BU)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L21
Chain IDs:U (auth: BV)
Chain Length:222
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uL22m
Chain IDs:V (auth: BW)
Chain Length:433
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uL23m
Chain IDs:W (auth: BX)
Chain Length:196
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:uL24m
Chain IDs:X (auth: BY)
Chain Length:216
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L37
Chain IDs:Y (auth: Ba)
Chain Length:1571
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L38
Chain IDs:Z (auth: Bb)
Chain Length:73
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L39
Chain IDs:AA (auth: Bc)
Chain Length:334
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L40
Chain IDs:BA (auth: Bd)
Chain Length:206
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L41
Chain IDs:CA (auth: Be)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mL42
Chain IDs:DA (auth: Bf)
Chain Length:294
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L43
Chain IDs:EA (auth: Bg)
Chain Length:159
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mL44
Chain IDs:FA (auth: Bh)
Chain Length:332
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L45
Chain IDs:GA (auth: Bi)
Chain Length:268
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L46
Chain IDs:HA (auth: Bj)
Chain Length:262
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L48, mitochondrial
Chain IDs:IA (auth: Bk)
Chain Length:269
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mrpl34
Chain IDs:JA (auth: Bl)
Chain Length:166
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L50
Chain IDs:KA (auth: Bm)
Chain Length:198
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L51
Chain IDs:LA (auth: Bn)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mL52
Chain IDs:MA (auth: Bo)
Chain Length:145
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mL53
Chain IDs:NA (auth: Bp)
Chain Length:112
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mL54
Chain IDs:OA (auth: Bq)
Chain Length:138
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L57
Chain IDs:PA (auth: Bt)
Chain Length:292
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mL62 (ICT1)
Chain IDs:QA (auth: Bu)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:mL64
Chain IDs:RA (auth: Bv)
Chain Length:222
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:39S ribosomal protein S30, mitochondrial
Chain IDs:SA (auth: Bw)
Chain Length:433
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S18A
Chain IDs:TA (auth: Bx)
Chain Length:196
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L12
Chain IDs:VA (auth: CL), WA (auth: DL), XA (auth: EL), LB (auth: FL), GC (auth: GL), HC (auth: HL)
Chain Length:198
Number of Molecules:6
Biological Source:Sus scrofa
Primary Citation
Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.
Mol.Cell 81 2566 2582.e6 (2021)
PMID: 33878294 DOI: 10.1016/j.molcel.2021.03.042

Abstact

The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.

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Primary Citation of related structures