› 8oiq

Electron Microscopy
3.5Å resolution

39S mammalian mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA

Released:
DOI: 10.2210/pdb8oiq/pdb
PDB entry 8oiq coloured by chain, front view.
PDB entry 8oiq coloured by chain, side view.
PDB entry 8oiq coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis of translation termination at noncanonical stop codons in human mitochondria.
Saurer M, Leibundgut M, Nadimpalli HP, Scaiola A, Schönhut T, Lee RG, Siira SJ, Rackham O, Dreos R, Lenarčič T, Kummer E, Gatfield D, Filipovska A, Ban N
Science 380 531-536 (2023)
PMID: 37141370
Related structures: EMD-16896

Function and Biology Details

Reaction catalysed: 
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 62-mer (preferred)
PDBe Complex ID:
PDB-CPX-246158 (preferred)
Entry contents:
53 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (57 distinct):
39S ribosomal protein L12, mitochondrial Chains: B1, B2, B3, B4, B5, B6
Molecule details ›
Chains: B1, B2, B3, B4, B5, B6
Length: 198 amino acids
Theoretical weight: 21.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0VGD9 (Residues: 1-198; Coverage: 100%)
Gene name: MRPL12
Sequence domains:
Large ribosomal subunit protein uL22m Chain: BA
Molecule details ›
Chain: BA
Length: 210 amino acids
Theoretical weight: 24.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TXR4 (Residues: 1-210; Coverage: 100%)
Gene name: MRPL22
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23m Chain: BB
Molecule details ›
Chain: BB
Length: 150 amino acids
Theoretical weight: 17.69 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480JJI1 (Residues: 1-150; Coverage: 100%)
Gene name: MRPL23
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24m Chain: BC
Molecule details ›
Chain: BC
Length: 216 amino acids
Theoretical weight: 24.89 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RHJ1 (Residues: 1-216; Coverage: 100%)
Gene name: MRPL24
Sequence domains:
39S ribosomal protein L27, mitochondrial Chain: BD
Molecule details ›
Chain: BD
Length: 148 amino acids
Theoretical weight: 15.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1U0F6 (Residues: 1-148; Coverage: 100%)
Gene name: MRPL27
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28m Chain: BE
Molecule details ›
Chain: BE
Length: 256 amino acids
Theoretical weight: 30.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZTW8 (Residues: 1-256; Coverage: 100%)
Gene name: MRPL28
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29m Chain: BF
Molecule details ›
Chain: BF
Length: 250 amino acids
Theoretical weight: 29.89 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SGC7 (Residues: 1-250; Coverage: 100%)
Gene name: MRPL47
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
Large ribosomal subunit protein uL30m Chain: BG
Molecule details ›
Chain: BG
Length: 161 amino acids
Theoretical weight: 18.92 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0VJF4 (Residues: 1-161; Coverage: 100%)
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32m Chain: BH
Molecule details ›
Chain: BH
Length: 207 amino acids
Theoretical weight: 23.57 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LTC4 (Residues: 1-207; Coverage: 100%)
Gene name: MRPL32
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33m Chain: BI
Molecule details ›
Chain: BI
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TLP9 (Residues: 1-65; Coverage: 100%)
Gene name: MRPL33
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34m Chain: BJ
Molecule details ›
Chain: BJ
Length: 95 amino acids
Theoretical weight: 10.87 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1JE64 (Residues: 1-95; Coverage: 100%)
Gene name: MRPL34
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35m Chain: BK
Molecule details ›
Chain: BK
Length: 188 amino acids
Theoretical weight: 21.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A5G2QZK0 (Residues: 1-188; Coverage: 100%)
Gene name: MRPL35
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein uL2 C-terminal domain-containing protein Chain: BL
Molecule details ›
Chain: BL
Length: 306 amino acids
Theoretical weight: 33.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287A143 (Residues: 1-306; Coverage: 100%)
Gene name: MRPL2
Sequence domains:
Large ribosomal subunit protein uL3m Chain: BM
Molecule details ›
Chain: BM
Length: 399 amino acids
Theoretical weight: 43.71 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A140UHW4 (Residues: 1-399; Coverage: 100%)
Gene name: MRPL3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4m Chain: BN
Molecule details ›
Chain: BN
Length: 294 amino acids
Theoretical weight: 33.25 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287B9C4 (Residues: 1-250; Coverage: 92%)
Gene name: MRPL4
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein bL9m Chain: BO
Molecule details ›
Chain: BO
Length: 268 amino acids
Theoretical weight: 30.37 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LR45 (Residues: 1-268; Coverage: 100%)
Gene name: MRPL9
Sequence domains:
Large ribosomal subunit protein uL10m Chain: BP
Molecule details ›
Chain: BP
Length: 257 amino acids
Theoretical weight: 29.24 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RWJ0 (Residues: 1-257; Coverage: 100%)
Gene name: MRPL10
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL11m Chain: BQ
Molecule details ›
Chain: BQ
Length: 192 amino acids
Theoretical weight: 20.81 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RU54 (Residues: 1-41, 42-160; Coverage: 100%)
Gene name: MRPL11
Sequence domains: Ribosomal protein L11, RNA binding domain
39S ribosomal protein L13, mitochondrial Chain: BR
Molecule details ›
Chain: BR
Length: 197 amino acids
Theoretical weight: 22.99 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GP19 (Residues: 1-197; Coverage: 100%)
Gene name: MRPL13
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14m Chain: BS
Molecule details ›
Chain: BS
Length: 325 amino acids
Theoretical weight: 34.8 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BMZ6 (Residues: 1-325; Coverage: 100%)
Gene name: MRPL14
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15m Chain: BT
Molecule details ›
Chain: BT
Length: 296 amino acids
Theoretical weight: 33.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0HMG9 (Residues: 1-296; Coverage: 100%)
Gene name: MRPL15
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16m Chain: BU
Molecule details ›
Chain: BU
Length: 251 amino acids
Theoretical weight: 28.68 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RI89 (Residues: 1-251; Coverage: 100%)
Gene name: MRPL16
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17m Chain: BV
Molecule details ›
Chain: BV
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RMQ4 (Residues: 1-169; Coverage: 100%)
Gene name: MRPL17
Sequence domains: Ribosomal protein L17
39S ribosomal protein L18, mitochondrial Chain: BW
Molecule details ›
Chain: BW
Length: 188 amino acids
Theoretical weight: 21.42 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VX01 (Residues: 1-188; Coverage: 100%)
Gene name: MRPL18
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19m Chain: BX
Molecule details ›
Chain: BX
Length: 303 amino acids
Theoretical weight: 34.53 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LNJ0 (Residues: 1-303; Coverage: 100%)
Gene name: MRPL19
Sequence domains: Ribosomal protein L19
39S ribosomal protein L20, mitochondrial isoform 1 Chain: BY
Molecule details ›
Chain: BY
Length: 149 amino acids
Theoretical weight: 17.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZU56 (Residues: 1-149; Coverage: 100%)
Gene name: MRPL20
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21m Chain: BZ
Molecule details ›
Chain: BZ
Length: 209 amino acids
Theoretical weight: 23.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RY70 (Residues: 1-209; Coverage: 100%)
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein mL52 Chain: Ba
Molecule details ›
Chain: Ba
Length: 160 amino acids
Theoretical weight: 17.99 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S9B7 (Residues: 1-160; Coverage: 100%)
Gene name: MRPL52
Sequence domains: Mitoribosomal protein mL52
Large ribosomal subunit protein mL53 Chain: Bb
Molecule details ›
Chain: Bb
Length: 112 amino acids
Theoretical weight: 12.06 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0LKT0 (Residues: 1-112; Coverage: 100%)
Sequence domains: 39S ribosomal protein L53/MRP-L53
Large ribosomal subunit protein mL54 Chain: Bc
Molecule details ›
Chain: Bc
Length: 138 amino acids
Theoretical weight: 15.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LN63 (Residues: 1-160; Coverage: 86%)
Gene name: MRPL54
Sequence domains: Mitochondrial ribosomal protein L37
Mitochondrial ribosomal protein L55 Chain: Bd
Molecule details ›
Chain: Bd
Length: 126 amino acids
Theoretical weight: 15.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1ULI6 (Residues: 1-126; Coverage: 100%)
Gene name: MRPL55
Sequence domains: Mitochondrial ribosomal protein L55
Mitochondrial ribosomal protein L57 Chain: Be
Molecule details ›
Chain: Be
Length: 102 amino acids
Theoretical weight: 12 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BP93 (Residues: 1-102; Coverage: 100%)
Gene name: MRPL57
Sequence domains: Mitochondrial ribosome protein 63
Large ribosomal subunit protein mL62 Chain: Bf
Molecule details ›
Chain: Bf
Length: 205 amino acids
Theoretical weight: 23.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZJR2 (Residues: 1-205; Coverage: 100%)
Gene name: MRPL58
Sequence domains: RF-1 domain
Large ribosomal subunit protein mL64 Chain: Bg
Molecule details ›
Chain: Bg
Length: 222 amino acids
Theoretical weight: 25.82 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZXA6 (Residues: 1-222; Coverage: 100%)
Gene name: GADD45GIP1
Sequence domains: Growth arrest and DNA-damage-inducible proteins-interacting protein 1
Mitochondrial ribosomal protein S18A Chain: Bh
Molecule details ›
Chain: Bh
Length: 196 amino acids
Theoretical weight: 22.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RRH6 (Residues: 9-25, 26-181; Coverage: 95%)
Gene name: MRPS18A
Sequence domains: Ribosomal protein S18
Mitochondrial ribosomal protein S30 Chain: Bi
Molecule details ›
Chain: Bi
Length: 433 amino acids
Theoretical weight: 49.1 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480QIM3 (Residues: 1-433; Coverage: 100%)
Gene name: MRPS30
Sequence domains: Mitochondrial 28S ribosomal protein S30 (PDCD9)
Large ribosomal subunit protein uL1m Chain: Bj
Molecule details ›
Chain: Bj
Length: 304 amino acids
Theoretical weight: 34.37 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AF82 (Residues: 1-304; Coverage: 100%)
Gene name: MRPL1
Sequence domains: Ribosomal protein L1p/L10e family
Ribosomal protein Chain: Bl
Molecule details ›
Chain: Bl
Length: 100 amino acids
Theoretical weight: 10.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287A731 (Residues: 1-100; Coverage: 100%)
Gene name: MRPL36
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein mL37 Chain: Bm
Molecule details ›
Chain: Bm
Length: 423 amino acids
Theoretical weight: 47.92 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BIV6 (Residues: 1-423; Coverage: 100%)
Gene name: MRPL37
Sequence domains: Mitochondrial 28S ribosomal protein S30 (PDCD9)
Large ribosomal subunit protein mL38 Chain: Bn
Molecule details ›
Chain: Bn
Length: 380 amino acids
Theoretical weight: 44.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RW03 (Residues: 1-380; Coverage: 100%)
Gene name: MRPL38
Sequence domains: Phosphatidylethanolamine-binding protein
TGS domain-containing protein Chain: Bo
Molecule details ›
Chain: Bo
Length: 334 amino acids
Theoretical weight: 38.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SHP6 (Residues: 1-303, 304-318; Coverage: 100%)
Gene name: MRPL39
Large ribosomal subunit protein mL40 Chain: Bp
Molecule details ›
Chain: Bp
Length: 162 amino acids
Theoretical weight: 19.41 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZP98 (Residues: 1-162; Coverage: 100%)
Gene name: MRPL40
Sequence domains: Mitochondrial ribosomal protein L28
39S ribosomal protein L41, mitochondrial Chain: Bq
Molecule details ›
Chain: Bq
Length: 135 amino acids
Theoretical weight: 15.07 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1BPA5 (Residues: 1-135; Coverage: 100%)
Sequence domains: Mitochondrial ribosomal protein L27
Large ribosomal subunit protein mL42 Chain: Br
Molecule details ›
Chain: Br
Length: 142 amino acids
Theoretical weight: 16.68 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BQA1 (Residues: 1-142; Coverage: 100%)
Gene name: MRPL42
Sequence domains: Mitochondrial 28S ribosomal protein S32
Large ribosomal subunit protein mL43 Chain: Bs
Molecule details ›
Chain: Bs
Length: 159 amino acids
Theoretical weight: 17.62 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S8U4 (Residues: 2-159; Coverage: 99%)
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Large ribosomal subunit protein mL44 Chain: Bt
Molecule details ›
Chain: Bt
Length: 332 amino acids
Theoretical weight: 37.53 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SR64 (Residues: 1-332; Coverage: 100%)
Gene name: MRPL44
Sequence domains:
Large ribosomal subunit protein mL45 Chain: Bu
Molecule details ›
Chain: Bu
Length: 306 amino acids
Theoretical weight: 35.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGM5 (Residues: 1-306; Coverage: 100%)
Gene name: MRPL45
Sequence domains: Tim44-like domain
Large ribosomal subunit protein mL46 Chain: Bv
Molecule details ›
Chain: Bv
Length: 279 amino acids
Theoretical weight: 32.22 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SRT0 (Residues: 1-279; Coverage: 100%)
Gene name: MRPL46
Sequence domains: 39S mitochondrial ribosomal protein L46
Small ribosomal subunit protein uS10 domain-containing protein Chain: Bw
Molecule details ›
Chain: Bw
Length: 269 amino acids
Theoretical weight: 29.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480J9Z6 (Residues: 1-269; Coverage: 100%)
Gene name: MRPL48
Sequence domains: Ribosomal protein S10p/S20e
Large ribosomal subunit protein mL49 Chain: Bx
Molecule details ›
Chain: Bx
Length: 166 amino acids
Theoretical weight: 18.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287A0K2 (Residues: 1-166; Coverage: 100%)
Gene name: MRPL49
Sequence domains: Mitochondrial large subunit ribosomal protein (Img2)
Large ribosomal subunit protein mL50 Chain: By
Molecule details ›
Chain: By
Length: 198 amino acids
Theoretical weight: 22.79 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3L9H6 (Residues: 1-198; Coverage: 100%)
Gene name: MRPL50
Sequence domains: Ribosomal subunit 39S
Large ribosomal subunit protein mL51 Chain: Bz
Molecule details ›
Chain: Bz
Length: 128 amino acids
Theoretical weight: 15.25 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1VKN8 (Residues: 1-128; Coverage: 100%)
Sequence domains: Mitochondrial ribosomal subunit
Peptide chain release factor 1, mitochondrial Chain: Aa
Molecule details ›
Chain: Aa
Length: 474 amino acids
Theoretical weight: 55.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75570 (Residues: 1-445; Coverage: 100%)
Gene name: MTRF1
Sequence domains:
E-site tRNA Chain: B7
Molecule details ›
Chain: B7
Length: 3 nucleotides
Theoretical weight: 895 Da
16S ribosomal RNA Chain: B8
Molecule details ›
Chain: B8
Length: 1571 nucleotides
Theoretical weight: 504.91 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
CP Phe-tRNA Chain: B9
Molecule details ›
Chain: B9
Length: 73 nucleotides
Theoretical weight: 23.52 KDa
Sequence domains: tRNA
P-site Met-tRNA(fMet) Chain: AG
Molecule details ›
Chain: AG
Length: 71 nucleotides
Theoretical weight: 22.66 KDa

Ligands and Environments

6 bound ligands:
Ligand MG 205 x MG
Ligand K 30 x K
Ligand PHE 1 x PHE
Ligand ZN 2 x ZN
Ligand FES 1 x FES
Ligand FME 1 x FME
7 modified residues:
Ligand 1MA 1 x 1MA
Ligand OMG 2 x OMG
Ligand OMU 1 x OMU
Ligand PSU 1 x PSU
Ligand MIA 1 x MIA
Ligand AYA 2 x AYA
Ligand SAC 1 x SAC

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-16896
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Decoding the Enigma: Translation Termination in Human Mitochondria.
Krüger et al. (2024)
1 more