7NSH image
Deposition Date 2021-03-07
Release Date 2021-05-05
Last Version Date 2024-07-10
Entry Detail
PDB ID:
7NSH
Keywords:
TRANSLATION
Title:
39S mammalian mitochondrial large ribosomal subunit with mtRRF (post) and mtEFG2
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7NSH validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L27
Chain IDs:A (auth: B0)
Chain Length:148
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1U0F6 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L28
Gene (Uniprot):MRPL28
Chain IDs:AA (auth: B1)
Chain Length:256
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZTW8 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L47
Gene (Uniprot):MRPL47
Chain IDs:IA (auth: B2)
Chain Length:252
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SGC7 Pfam ID:PF06984
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL30m
Chain IDs:JA (auth: B3)
Chain Length:161
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1MIP3 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:bL31m
Chain IDs:KA (auth: B4)
Chain Length:126
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1ULI6 Pfam ID:PF09776
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:bL32m
Gene (Uniprot):MRPL32
Chain IDs:LA (auth: B5)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LTC4 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:bL33m
Chain IDs:MA (auth: B6)
Chain Length:65
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TLP9 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L34
Chain IDs:NA (auth: B7)
Chain Length:95
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1UFR4 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L35
Gene (Uniprot):MRPL35
Chain IDs:D (auth: B8)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SVC5
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Gene (Uniprot):MRPL36
Chain IDs:EA (auth: B9)
Chain Length:100
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287A731 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:HA (auth: BA)
Chain Length:1571
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polyribonucleotide
Molecule:CP tRNAPhe
Chain IDs:OA (auth: BB)
Chain Length:73
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome-releasing factor 2, mitochondrial
Gene (Uniprot):GFM2
Chain IDs:PA (auth: BC)
Chain Length:334
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q969S9 Pfam ID:PF00009, PF22042, PF14492, PF03764, PF00679
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL2m
Gene (Uniprot):MRPL2
Chain IDs:QA (auth: BD)
Chain Length:206
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RRN2 Pfam ID:PF00181
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ICT1
Gene (Uniprot):MRPL3
Chain IDs:UA (auth: BE)
Chain Length:399
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A140UHW4 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L4
Gene (Uniprot):MRPL4
Chain IDs:VA (auth: BF)
Chain Length:294
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287B9C4 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome-recycling factor, mitochondrial
Gene (Uniprot):MRRF
Chain IDs:RA (auth: BG)
Chain Length:159
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96E11 Pfam ID:PF01765
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L9
Gene (Uniprot):MRPL9
Chain IDs:WA (auth: BI)
Chain Length:268
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LR45 Pfam ID:PF01281, PF22078
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L10
Gene (Uniprot):MRPL10
Chain IDs:XA (auth: BJ)
Chain Length:279
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RWJ0 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L11
Gene (Uniprot):MRPL11
Chain IDs:YA (auth: BK)
Chain Length:192
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RU54 Pfam ID:PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL13m
Gene (Uniprot):MRPL13
Chain IDs:ZA (auth: BN)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:K7GP19 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL14m
Gene (Uniprot):MRPL14
Chain IDs:AB (auth: BO)
Chain Length:124
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287BMZ6 Pfam ID:PF00238
Polymer Type:polypeptide(L)
Molecule:uL15m
Chain IDs:BB (auth: BP)
Chain Length:112
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL16m
Gene (Uniprot):MRPL16
Chain IDs:SA (auth: BQ)
Chain Length:138
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RI89 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:bL17m
Gene (Uniprot):MRPL17
Chain IDs:CB (auth: BR)
Chain Length:169
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RMQ4 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L18
Gene (Uniprot):MRPL18
Chain IDs:DB (auth: BS)
Chain Length:180
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZNK1 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L19
Gene (Uniprot):MRPL19
Chain IDs:EB (auth: BT)
Chain Length:292
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LNJ0 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L20
Gene (Uniprot):MRPL20
Chain IDs:FB (auth: BU)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZU56 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L21
Chain IDs:GB (auth: BV)
Chain Length:222
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RY70 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL22m
Chain IDs:HB (auth: BW)
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TXR4 Pfam ID:PF00237
Polymer Type:polypeptide(L)
Molecule:uL23m
Chain IDs:IB (auth: BX)
Chain Length:150
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL24m
Gene (Uniprot):MRPL24
Chain IDs:B (auth: BY)
Chain Length:216
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RHJ1 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L37
Gene (Uniprot):MRPL37
Chain IDs:C (auth: Ba)
Chain Length:1571
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287BIV6 Pfam ID:PF07147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L38
Gene (Uniprot):MRPL38
Chain IDs:E (auth: Bb)
Chain Length:73
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RW03 Pfam ID:PF01161
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L39
Gene (Uniprot):MRPL39
Chain IDs:F (auth: Bc)
Chain Length:334
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SHP6
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L40
Gene (Uniprot):MRPL40
Chain IDs:G (auth: Bd)
Chain Length:206
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A5G2R2V2 Pfam ID:PF09812
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L41
Chain IDs:H (auth: Be)
Chain Length:399
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1F1K9 Pfam ID:PF09809
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL42
Gene (Uniprot):MRPL42
Chain IDs:I (auth: Bf)
Chain Length:294
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287BQA1 Pfam ID:PF10210
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L43
Gene (Uniprot):MRPL43
Chain IDs:J (auth: Bg)
Chain Length:159
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1S8U4 Pfam ID:PF05047
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL44
Gene (Uniprot):MRPL44
Chain IDs:K (auth: Bh)
Chain Length:332
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SR64 Pfam ID:PF22935, PF22892
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L45
Gene (Uniprot):MRPL45
Chain IDs:L (auth: Bi)
Chain Length:268
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LGM5 Pfam ID:PF04280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L46
Gene (Uniprot):MRPL46
Chain IDs:M (auth: Bj)
Chain Length:279
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SRT0 Pfam ID:PF11788
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L48, mitochondrial
Gene (Uniprot):MRPL48
Chain IDs:N (auth: Bk)
Chain Length:192
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A480J9Z6 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mrpl34
Gene (Uniprot):MRPL49
Chain IDs:O (auth: Bl)
Chain Length:166
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A0R4J8D6 Pfam ID:PF05046
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L50
Gene (Uniprot):MRPL50
Chain IDs:P (auth: Bm)
Chain Length:198
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3L9H6 Pfam ID:PF10501
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L51
Chain IDs:Q (auth: Bn)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1P1C8 Pfam ID:PF10244
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL52
Gene (Uniprot):MRPL52
Chain IDs:R (auth: Bo)
Chain Length:124
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1S9B7 Pfam ID:PF18699
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL53
Gene (Uniprot):MRPL53
Chain IDs:S (auth: Bp)
Chain Length:112
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A341D604 Pfam ID:PF10780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL54
Gene (Uniprot):MRPL54
Chain IDs:T (auth: Bq)
Chain Length:138
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LN63 Pfam ID:PF08561
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L57
Gene (Uniprot):MRPL57
Chain IDs:U (auth: Bt)
Chain Length:292
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287BP93 Pfam ID:PF14978
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL62 (ICT1)
Gene (Uniprot):MRPL58
Chain IDs:V (auth: Bu)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZJR2 Pfam ID:PF00472
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL64
Gene (Uniprot):GADD45GIP1
Chain IDs:W (auth: Bv)
Chain Length:222
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZXA6 Pfam ID:PF10147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S30, mitochondrial
Gene (Uniprot):MRPS30
Chain IDs:X (auth: Bw)
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A480QIM3 Pfam ID:PF07147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein S18A
Gene (Uniprot):MRPS18A
Chain IDs:Y (auth: Bx)
Chain Length:150
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RRH6 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L12
Chain IDs:Z (auth: CL), BA (auth: DL), CA (auth: EL), DA (auth: FL), FA (auth: GL), GA (auth: HL), TA (auth: LL)
Chain Length:198
Number of Molecules:7
Biological Source:Sus scrofa
UniProt ID:A0A4X1U6S6 Pfam ID:PF16320, PF00542
Ligand Molecules
5GP
GNP
MG
SPM
ZN
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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Disease

Primary Citation of related structures
7NSH
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