8OIQ image
Deposition Date 2023-03-23
Release Date 2023-06-14
Last Version Date 2024-06-26
Entry Detail
PDB ID:
8OIQ
Keywords:
RIBOSOME
Title:
39S mammalian mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8OIQ validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:P-site Met-tRNA(fMet)
Chain IDs:IB (auth: AG)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptide chain release factor 1, mitochondrial
Gene (Uniprot):MTRF1
Chain IDs:JB (auth: Aa)
Chain Length:474
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75570 Pfam ID:PF03462, PF00472
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L12
Gene (Uniprot):MRPL12
Chain IDs:A (auth: B1), B (auth: B2), C (auth: B3), D (auth: B4), E (auth: B5), F (auth: B6)
Chain Length:198
Number of Molecules:6
Biological Source:Sus scrofa
UniProt ID:A0A8D0VGD9 Pfam ID:PF16320, PF00542
Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:G (auth: B7)
Chain Length:3
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:H (auth: B8)
Chain Length:1571
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polyribonucleotide
Molecule:CP Phe-tRNA
Chain IDs:I (auth: B9)
Chain Length:73
Number of Molecules:1
Biological Source:Sus scrofa
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22m
Gene (Uniprot):MRPL22
Chain IDs:J (auth: BA)
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TXR4 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L23, mitochondrial
Gene (Uniprot):MRPL23
Chain IDs:K (auth: BB)
Chain Length:112
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A480JJI1 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL24m
Gene (Uniprot):MRPL24
Chain IDs:L (auth: BC)
Chain Length:138
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RHJ1 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L27, mitochondrial
Chain IDs:M (auth: BD)
Chain Length:148
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1U0F6 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L28
Gene (Uniprot):MRPL28
Chain IDs:N (auth: BE)
Chain Length:102
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZTW8 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L47
Gene (Uniprot):MRPL47
Chain IDs:O (auth: BF)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SGC7 Pfam ID:PF06984
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30m
Chain IDs:P (auth: BG)
Chain Length:222
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D0VJF4 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L32
Gene (Uniprot):MRPL32
Chain IDs:Q (auth: BH)
Chain Length:207
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LTC4 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33m
Gene (Uniprot):MRPL33
Chain IDs:R (auth: BI)
Chain Length:433
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TLP9 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34m
Gene (Uniprot):MRPL34
Chain IDs:S (auth: BJ)
Chain Length:95
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1JE64 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L35, mitochondrial
Gene (Uniprot):MRPL35
Chain IDs:T (auth: BK)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A5G2QZK0 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L2
Gene (Uniprot):MRPL2
Chain IDs:U (auth: BL)
Chain Length:306
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287A143 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ICT1
Gene (Uniprot):MRPL3
Chain IDs:V (auth: BM)
Chain Length:399
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A140UHW4 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L4
Gene (Uniprot):MRPL4
Chain IDs:W (auth: BN)
Chain Length:294
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287B9C4 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L9
Gene (Uniprot):MRPL9
Chain IDs:X (auth: BO)
Chain Length:268
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LR45 Pfam ID:PF01281, PF22078
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L10
Gene (Uniprot):MRPL10
Chain IDs:Y (auth: BP)
Chain Length:257
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RWJ0 Pfam ID:PF00466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L11
Gene (Uniprot):MRPL11
Chain IDs:Z (auth: BQ)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RU54 Pfam ID:PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L13, mitochondrial
Gene (Uniprot):MRPL13
Chain IDs:AA (auth: BR)
Chain Length:197
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:K7GP19 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L14
Gene (Uniprot):MRPL14
Chain IDs:BA (auth: BS)
Chain Length:159
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287BMZ6 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L15, mitochondrial
Chain IDs:CA (auth: BT)
Chain Length:296
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D0HMG9 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL16m
Gene (Uniprot):MRPL16
Chain IDs:DA (auth: BU)
Chain Length:251
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RI89 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:bL17m
Gene (Uniprot):MRPL17
Chain IDs:EA (auth: BV)
Chain Length:169
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RMQ4 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L18
Gene (Uniprot):MRPL18
Chain IDs:FA (auth: BW)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VX01 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L19, mitochondrial
Gene (Uniprot):MRPL19
Chain IDs:GA (auth: BX)
Chain Length:166
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LNJ0 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L20
Gene (Uniprot):MRPL20
Chain IDs:HA (auth: BY)
Chain Length:198
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZU56 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L21
Chain IDs:IA (auth: BZ)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RY70 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L52, mitochondrial
Gene (Uniprot):MRPL52
Chain IDs:JA (auth: Ba)
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1S9B7 Pfam ID:PF18699
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L53
Chain IDs:KA (auth: Bb)
Chain Length:112
Number of Molecules:1
Biological Source:Sus scrofa
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL54
Gene (Uniprot):MRPL54
Chain IDs:LA (auth: Bc)
Chain Length:138
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LN63 Pfam ID:PF08561
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L55
Gene (Uniprot):MRPL55
Chain IDs:MA (auth: Bd)
Chain Length:148
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1ULI6 Pfam ID:PF09776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L57
Gene (Uniprot):MRPL57
Chain IDs:NA (auth: Be)
Chain Length:102
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287BP93 Pfam ID:PF14978
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL62 (ICT1)
Gene (Uniprot):MRPL58
Chain IDs:OA (auth: Bf)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZJR2 Pfam ID:PF00472
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL64
Gene (Uniprot):GADD45GIP1
Chain IDs:PA (auth: Bg)
Chain Length:222
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZXA6 Pfam ID:PF10147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein S18A
Gene (Uniprot):MRPS18A
Chain IDs:QA (auth: Bh)
Chain Length:207
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RRH6 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S30, mitochondrial
Gene (Uniprot):MRPS30
Chain IDs:RA (auth: Bi)
Chain Length:433
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A480QIM3 Pfam ID:PF07147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L1, mitochondrial
Gene (Uniprot):MRPL1
Chain IDs:SA (auth: Bj)
Chain Length:95
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287AF82 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Gene (Uniprot):MRPL36
Chain IDs:TA (auth: Bl)
Chain Length:306
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287A731 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L37
Gene (Uniprot):MRPL37
Chain IDs:UA (auth: Bm)
Chain Length:399
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287BIV6 Pfam ID:PF07147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L38
Gene (Uniprot):MRPL38
Chain IDs:VA (auth: Bn)
Chain Length:294
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RW03 Pfam ID:PF01161
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L39
Gene (Uniprot):MRPL39
Chain IDs:WA (auth: Bo)
Chain Length:268
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SHP6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L40
Gene (Uniprot):MRPL40
Chain IDs:XA (auth: Bp)
Chain Length:257
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A286ZP98 Pfam ID:PF09812
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L41, mitochondrial
Chain IDs:YA (auth: Bq)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1BPA5 Pfam ID:PF09809
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL42
Gene (Uniprot):MRPL42
Chain IDs:ZA (auth: Br)
Chain Length:197
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287BQA1 Pfam ID:PF10210
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL43
Chain IDs:AB (auth: Bs)
Chain Length:159
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1S8U4 Pfam ID:PF05047
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL44
Gene (Uniprot):MRPL44
Chain IDs:BB (auth: Bt)
Chain Length:296
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SR64 Pfam ID:PF22935, PF22892
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L45
Gene (Uniprot):MRPL45
Chain IDs:CB (auth: Bu)
Chain Length:251
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LGM5 Pfam ID:PF04280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L46
Gene (Uniprot):MRPL46
Chain IDs:DB (auth: Bv)
Chain Length:169
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SRT0 Pfam ID:PF11788
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L48, mitochondrial
Gene (Uniprot):MRPL48
Chain IDs:EB (auth: Bw)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A480J9Z6 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L49, mitochondrial
Gene (Uniprot):MRPL49
Chain IDs:FB (auth: Bx)
Chain Length:166
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287A0K2 Pfam ID:PF05046
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L50
Gene (Uniprot):MRPL50
Chain IDs:GB (auth: By)
Chain Length:198
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3L9H6 Pfam ID:PF10501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL51
Chain IDs:HB (auth: Bz)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1VKN8 Pfam ID:PF10244
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA H A modified residue
AYA K ALA modified residue
OMG H G modified residue
OMU H U modified residue
PSU H U modified residue
SAC AA SER modified residue
Ligand Molecules
FES
FME
K
MG
PHE
ZN
Primary Citation
Molecular basis of translation termination at noncanonical stop codons in human mitochondria.
Science 380 531 536 (2023)
PMID: 37141370 DOI: 10.1126/science.adf9890

Abstact

The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.

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Protein

Chemical

Disease

Primary Citation of related structures
8OIQ