› 8oip

Electron Microscopy
3.6Å resolution

28S mammalian mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA

Released:
DOI: 10.2210/pdb8oip/pdb
PDB entry 8oip coloured by chain, front view.
PDB entry 8oip coloured by chain, side view.
PDB entry 8oip 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-16895

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
PDBe Complex ID:
PDB-CPX-236633 (preferred)
Entry contents:
33 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (36 distinct):
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
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
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein Chain: AB
Molecule details ›
Chain: AB
Length: 366 amino acids
Theoretical weight: 41.36 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SG95 (Residues: 1-366; Coverage: 100%)
Gene name: MRPS35
Sequence domains: Mitochondrial ribosomal subunit protein
Mitochondrial ribosomal protein S24 Chain: AC
Molecule details ›
Chain: AC
Length: 167 amino acids
Theoretical weight: 18.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ANU4 (Residues: 1-167; Coverage: 100%)
Gene name: MRPS24
Sequence domains: Mitochondrial ribosome subunit S24
Small ribosomal subunit protein mS38 Chain: AD
Molecule details ›
Chain: AD
Length: 199 amino acids
Theoretical weight: 22.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D2A802 (Residues: 1-199; Coverage: 100%)
Gene name: AURKAIP1
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein bS6m Chain: AE
Molecule details ›
Chain: AE
Length: 376 amino acids
Theoretical weight: 41.09 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TSM9 (Residues: 28-275; Coverage: 90%)
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7m Chain: AF
Molecule details ›
Chain: AF
Length: 242 amino acids
Theoretical weight: 28.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZJ25 (Residues: 1-242; Coverage: 100%)
Gene name: MRPS7
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS10m Chain: AH
Molecule details ›
Chain: AH
Length: 200 amino acids
Theoretical weight: 23.11 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RUU2 (Residues: 1-200; Coverage: 100%)
Gene name: MRPS10
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS12m Chain: AJ
Molecule details ›
Chain: AJ
Length: 139 amino acids
Theoretical weight: 15.26 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL52 (Residues: 1-139; Coverage: 100%)
Sequence domains: Ribosomal protein S12/S23
Mitochondrial ribosomal protein S14 Chain: AK
Molecule details ›
Chain: AK
Length: 128 amino acids
Theoretical weight: 15.12 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL53 (Residues: 1-128; Coverage: 100%)
Gene name: MRPS14
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15m Chain: AL
Molecule details ›
Chain: AL
Length: 259 amino acids
Theoretical weight: 29.6 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AKS1 (Residues: 1-259; Coverage: 100%)
Gene name: MRPS15
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16m Chain: AM
Molecule details ›
Chain: AM
Length: 135 amino acids
Theoretical weight: 15.18 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480JTD7 (Residues: 1-135; Coverage: 100%)
Sequence domains: Ribosomal protein S16
28S ribosomal protein S17, mitochondrial Chain: AN
Molecule details ›
Chain: AN
Length: 130 amino acids
Theoretical weight: 14.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1UDM1 (Residues: 1-130; Coverage: 100%)
Gene name: MRPS17
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein mS40 Chain: AO
Molecule details ›
Chain: AO
Length: 258 amino acids
Theoretical weight: 29.22 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q767K8 (Residues: 1-258; Coverage: 100%)
Gene name: MRPS18B
Sequence domains: Ribosomal protein S18
Mitochondrial ribosomal protein S18C Chain: AP
Molecule details ›
Chain: AP
Length: 143 amino acids
Theoretical weight: 16.21 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL54 (Residues: 1-143; Coverage: 100%)
Gene name: MRPS18C
Sequence domains: Ribosomal protein S18
28S ribosomal protein S21, mitochondrial Chain: AQ
Molecule details ›
Chain: AQ
Length: 87 amino acids
Theoretical weight: 10.72 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZNB3 (Residues: 1-87; Coverage: 100%)
Gene name: MRPS21
Sequence domains: Ribosomal protein S21
Mitochondrial ribosomal protein S22 Chain: AR
Molecule details ›
Chain: AR
Length: 382 amino acids
Theoretical weight: 43.23 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AQT5 (Residues: 1-382; Coverage: 100%)
Gene name: MRPS22
Sequence domains: Mitochondrial 28S ribosomal protein S22
Small ribosomal subunit protein mS23 conserved domain-containing protein Chain: AS
Molecule details ›
Chain: AS
Length: 190 amino acids
Theoretical weight: 21.67 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AEW3 (Residues: 17-207; Coverage: 91%)
Gene name: MRPS23
Sequence domains: Mitochondrial ribosomal protein S23
Small ribosomal subunit protein mS25 Chain: AT
Molecule details ›
Chain: AT
Length: 173 amino acids
Theoretical weight: 19.95 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL55 (Residues: 1-173; Coverage: 100%)
Gene name: MRPS25
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Progonadoliberin Chain: AU
Molecule details ›
Chain: AU
Length: 205 amino acids
Theoretical weight: 23.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AY01 (Residues: 54-77; Coverage: 22%)
Gene name: GNRH2
Mitochondrial ribosomal protein S27 Chain: AV
Molecule details ›
Chain: AV
Length: 395 amino acids
Theoretical weight: 45.76 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A5G2R1I0 (Residues: 1-395; Coverage: 100%)
Gene name: MRPS27
Sequence domains: Mitochondrial 28S ribosomal protein S27
28S ribosomal protein S28, mitochondrial Chain: AW
Molecule details ›
Chain: AW
Length: 188 amino acids
Theoretical weight: 21.01 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL56 (Residues: 1-188; Coverage: 100%)
Gene name: MRPS28
Sequence domains: Mitochondrial ribosomal protein MRP-S35
Small ribosomal subunit protein mS29 Chain: AX
Molecule details ›
Chain: AX
Length: 410 amino acids
Theoretical weight: 46.97 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1XNL0 (Residues: 1-410; Coverage: 100%)
Gene name: DAP3
Sequence domains: Mitochondrial ribosomal death-associated protein 3
Small ribosomal subunit protein mS31 Chain: AY
Molecule details ›
Chain: AY
Length: 381 amino acids
Theoretical weight: 43.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RME2 (Residues: 1-381; Coverage: 100%)
Gene name: MRPS31
Sequence domains: Mitochondrial 28S ribosomal protein S31
Small ribosomal subunit protein mS33 Chain: AZ
Molecule details ›
Chain: AZ
Length: 148 amino acids
Theoretical weight: 16.97 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1V2H3 (Residues: 1-148; Coverage: 100%)
Gene name: MRPS33
Sequence domains: Mitochondrial ribosomal subunit S27
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:
Mitochondrial ribosomal protein S2 Chain: Ab
Molecule details ›
Chain: Ab
Length: 289 amino acids
Theoretical weight: 31.73 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S001 (Residues: 1-289; Coverage: 100%)
Gene name: MRPS2
Sequence domains: Ribosomal protein S2
CHCH domain-containing protein Chain: Ac
Molecule details ›
Chain: Ac
Length: 118 amino acids
Theoretical weight: 13.6 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1SZV4 (Residues: 1-118; Coverage: 100%)
Gene name: CHCHD1
Sequence domains: CHCH domain
Small ribosomal subunit protein uS5m Chain: Ad
Molecule details ›
Chain: Ad
Length: 430 amino acids
Theoretical weight: 48.21 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SU66 (Residues: 1-430; Coverage: 100%)
Gene name: MRPS5
Sequence domains:
Small ribosomal subunit protein mS39 Chain: Ae
Molecule details ›
Chain: Ae
Length: 692 amino acids
Theoretical weight: 78.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GKS8 (Residues: 1-546, 547-690; Coverage: 100%)
Gene name: PTCD3
Sequence domains:
28S ribosomal protein S9, mitochondrial Chain: Ag
Molecule details ›
Chain: Ag
Length: 397 amino acids
Theoretical weight: 45.6 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LU08 (Residues: 1-397; Coverage: 100%)
Gene name: MRPS9
Sequence domains: Ribosomal protein S9/S16
Mitochondrial ribosomal protein S11 Chain: Ai
Molecule details ›
Chain: Ai
Length: 196 amino acids
Theoretical weight: 20.86 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZJJ6 (Residues: 1-196; Coverage: 100%)
Gene name: MRPS11
Sequence domains: Ribosomal protein S11
Mitochondrial ribosomal protein S34 Chain: Aj
Molecule details ›
Chain: Aj
Length: 505 amino acids
Theoretical weight: 55.71 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AVS9 (Residues: 1-505; Coverage: 100%)
Gene name: MRPS34
Sequence domains: Mitochondrial 28S ribosomal protein S34
12S rRNA Chain: AA
Molecule details ›
Chain: AA
Length: 962 nucleotides
Theoretical weight: 309.09 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-site Met-tRNA(fMet) Chain: AG
Molecule details ›
Chain: AG
Length: 72 nucleotides
Theoretical weight: 22.82 KDa
Messenger RNA Chain: AI
Molecule details ›
Chain: AI
Length: 9 nucleotides
Theoretical weight: 2.9 KDa

Ligands and Environments

8 bound ligands:
Ligand MG 127 x MG
Ligand SPM 1 x SPM
Ligand SPD 1 x SPD
Ligand K 11 x K
Ligand ZN 1 x ZN
Ligand FS2 2 x FS2
Ligand ATP 1 x ATP
Ligand GDP 1 x GDP
6 modified residues:
Ligand 5MU 1 x 5MU
Ligand B8T 1 x B8T
Ligand 5MC 1 x 5MC
Ligand MA6 2 x MA6
Ligand FME 1 x FME
Ligand AYA 2 x AYA

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-16895
Expression system: Homo sapiens

Quick links

Citations

2 citation in other articles

Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes.
Tetzlaff et al. (2024)
1 more