› 8om2

Electron Microscopy
2.57Å resolution

Small subunit of yeast mitochondrial ribosome in complex with METTL17/Rsm22.

Released:
DOI: 10.2210/pdb8om2/pdb
PDB entry 8om2 coloured by chain, front view.
PDB entry 8om2 coloured by chain, side view.
PDB entry 8om2 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
METTL17 is an Fe-S cluster checkpoint for mitochondrial translation.
Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK
Mol Cell (2024)
PMID: 38199006
Related structures: EMD-16966

Function and Biology Details

Reaction catalysed: 
3-hydroxy-2-methylpropanoyl-CoA + H(2)O = CoA + 3-hydroxy-2-methylpropanoate
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero 35-mer (preferred)
PDBe Complex ID:
PDB-CPX-271817 (preferred)
Entry contents:
34 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (35 distinct):
Small ribosomal subunit protein bS1m Chain: A
Molecule details ›
Chain: A
Length: 344 amino acids
Theoretical weight: 39.51 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02950 (Residues: 1-344; Coverage: 100%)
Gene names: MRP51, YPL118W
Sequence domains: Mitochondrial ribosomal protein subunit
Small ribosomal subunit protein uS2m Chain: B
Molecule details ›
Chain: B
Length: 394 amino acids
Theoretical weight: 44.21 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32902 (Residues: 1-394; Coverage: 100%)
Gene names: MRP4, MRP4A, YHL004W
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3m Chain: C
Molecule details ›
Chain: C
Length: 398 amino acids
Theoretical weight: 47.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02381 (Residues: 1-398; Coverage: 100%)
Gene names: Q0140, VAR1
Sequence domains: Mitochondrial ribosomal protein (VAR1)
Small ribosomal subunit protein uS4m Chain: D
Molecule details ›
Chain: D
Length: 486 amino acids
Theoretical weight: 56.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P27929 (Residues: 1-486; Coverage: 100%)
Gene names: MNA6, N1211, N1840, NAM9, YNL137C
Sequence domains: S4 domain
Small ribosomal subunit protein uS5m Chain: E
Molecule details ›
Chain: E
Length: 307 amino acids
Theoretical weight: 34.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33759 (Residues: 1-307; Coverage: 100%)
Gene names: MRPS5, YBR1704, YBR251W
Sequence domains:
Small ribosomal subunit protein bS6m Chain: F
Molecule details ›
Chain: F
Length: 131 amino acids
Theoretical weight: 15.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28778 (Residues: 1-131; Coverage: 100%)
Gene names: MRP17, YKL003C
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7m Chain: G
Molecule details ›
Chain: G
Length: 247 amino acids
Theoretical weight: 27.86 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P47150 (Residues: 1-247; Coverage: 100%)
Gene names: J2020, RSM7, YJR113C
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8m Chain: H
Molecule details ›
Chain: H
Length: 154 amino acids
Theoretical weight: 17.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03799 (Residues: 2-155; Coverage: 99%)
Gene names: MRPS8, YM8520.07, YMR158W
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9m Chain: I
Molecule details ›
Chain: I
Length: 278 amino acids
Theoretical weight: 31.98 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38120 (Residues: 1-278; Coverage: 100%)
Gene names: MRPS9, YBR1123, YBR146W
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10m Chain: J
Molecule details ›
Chain: J
Length: 203 amino acids
Theoretical weight: 23.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03201 (Residues: 1-203; Coverage: 100%)
Gene names: RSM10, YD6888.03, YDR041W
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11m Chain: K
Molecule details ›
Chain: K
Length: 217 amino acids
Theoretical weight: 24.6 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P42847 (Residues: 1-217; Coverage: 100%)
Gene names: MRPS18, N0397, YNL306W
Small ribosomal subunit protein uS12m Chain: L
Molecule details ›
Chain: L
Length: 153 amino acids
Theoretical weight: 16.95 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53732 (Residues: 1-153; Coverage: 100%)
Gene names: MRPS12, N3298, YNR036C
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13m Chain: M
Molecule details ›
Chain: M
Length: 143 amino acids
Theoretical weight: 16.09 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53937 (Residues: 1-143; Coverage: 100%)
Gene names: N2322, SWS2, YNL081C
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14m Chain: N
Molecule details ›
Chain: N
Length: 115 amino acids
Theoretical weight: 13.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10663 (Residues: 1-115; Coverage: 100%)
Gene names: MRP2, P9325.7, YPR166C
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15m Chain: O
Molecule details ›
Chain: O
Length: 286 amino acids
Theoretical weight: 33.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21771 (Residues: 1-286; Coverage: 100%)
Gene names: D9651.3, MRPS28, YDR337W
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16m Chain: P
Molecule details ›
Chain: P
Length: 121 amino acids
Theoretical weight: 13.66 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02608 (Residues: 1-121; Coverage: 100%)
Gene names: LPA4C, MRPS16, YPL013C
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17m Chain: Q
Molecule details ›
Chain: Q
Length: 237 amino acids
Theoretical weight: 27.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03246 (Residues: 1-237; Coverage: 100%)
Gene names: MRPS17, YM8010.18C, YMR188C
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18m Chain: R
Molecule details ›
Chain: R
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40033 (Residues: 1-138; Coverage: 100%)
Gene names: RSM18, YER050C
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19m Chain: S
Molecule details ›
Chain: S
Length: 91 amino acids
Theoretical weight: 10.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53733 (Residues: 1-91; Coverage: 100%)
Gene names: N3300, RSM19, YNR037C
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS21m Chain: T
Molecule details ›
Chain: T
Length: 177 amino acids
Theoretical weight: 20.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38175 (Residues: 1-177; Coverage: 100%)
Gene names: MRP21, MRP50, YBL0702, YBL090W
Sequence domains: Ribosomal protein S21
Small ribosomal subunit protein mS23 Chain: U
Molecule details ›
Chain: U
Length: 264 amino acids
Theoretical weight: 30.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40496 (Residues: 1-264; Coverage: 100%)
Gene names: RSM25, YIL093C
Sequence domains: Mitochondrial ribosomal protein S25
Small ribosomal subunit protein mS26 Chain: V
Molecule details ›
Chain: V
Length: 318 amino acids
Theoretical weight: 36.06 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P17558 (Residues: 1-318; Coverage: 100%)
Gene names: PET123, YOR158W
Small ribosomal subunit protein mS29 Chain: W
Molecule details ›
Chain: W
Length: 450 amino acids
Theoretical weight: 50.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01163 (Residues: 1-450; Coverage: 100%)
Gene names: G2856, RSM23, YGL129C
Sequence domains: Mitochondrial ribosomal death-associated protein 3
Small ribosomal subunit protein mS33 Chain: X
Molecule details ›
Chain: X
Length: 110 amino acids
Theoretical weight: 12.42 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53305 (Residues: 1-110; Coverage: 100%)
Gene names: RSM27, YGR215W
Sequence domains: Mitochondrial ribosomal subunit S27
Small ribosomal subunit protein mS35 Chain: Y
Molecule details ›
Chain: Y
Length: 319 amino acids
Theoretical weight: 37.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03976 (Residues: 1-319; Coverage: 100%)
Gene names: RSM24, YDR175C
Sequence domains: Mitochondrial ribosomal subunit protein
Small ribosomal subunit protein mS37 Chain: Z
Molecule details ›
Chain: Z
Length: 95 amino acids
Theoretical weight: 10.71 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O75012 (Residues: 1-95; Coverage: 100%)
Gene names: MRP10, YDL045W-A
Sequence domains: CHCH domain
Small ribosomal subunit protein mS38 Chain: 1
Molecule details ›
Chain: 1
Length: 111 amino acids
Theoretical weight: 12.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32344 (Residues: 1-111; Coverage: 100%)
Gene names: COX24, QRI5, YLR204W
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein mS41 Chain: 2
Molecule details ›
Chain: 2
Length: 130 amino acids
Theoretical weight: 15.32 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38783 (Residues: 1-130; Coverage: 100%)
Gene names: FYV4, YHR059W
Sequence domains: IGR protein motif
Small ribosomal subunit protein mS42 Chain: 3
Molecule details ›
Chain: 3
Length: 266 amino acids
Theoretical weight: 30.26 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P47141 (Residues: 1-266; Coverage: 100%)
Gene names: J1952, RSM26, YJR101W
Sequence domains: Iron/manganese superoxide dismutases, C-terminal domain
Small ribosomal subunit protein mS43 Chain: 4
Molecule details ›
Chain: 4
Length: 321 amino acids
Theoretical weight: 36.78 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10662 (Residues: 1-321; Coverage: 100%)
Gene names: D9651.1, MRP1, YDR347W
Small ribosomal subunit protein mS27 Chain: 5
Molecule details ›
Chain: 5
Length: 339 amino acids
Theoretical weight: 39.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P12686 (Residues: 1-339; Coverage: 100%)
Gene names: MRP13, YGR084C
Small ribosomal subunit protein mS45 Chain: 6
Molecule details ›
Chain: 6
Length: 345 amino acids
Theoretical weight: 39.64 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53292 (Residues: 1-345; Coverage: 100%)
Gene names: MRPS35, YGR165W
Sequence domains: Eukaryotic mitochondrial regulator protein
Small ribosomal subunit protein mS47 Chain: 8
Molecule details ›
Chain: 8
Length: 500 amino acids
Theoretical weight: 56.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28817 (Residues: 1-500; Coverage: 100%)
Gene names: EHD3, MRP5, YD9673.08C, YDR036C
Sequence domains: Enoyl-CoA hydratase/isomerase
Ribosome assembly protein RSM22, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 628 amino acids
Theoretical weight: 72.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36056 (Residues: 1-628; Coverage: 100%)
Gene names: RSM22, YKL155C, YKL610
Sequence domains: Mitochondrial small ribosomal subunit Rsm22
15S mitochondrial rRNA Chain: r
Molecule details ›
Chain: r
Length: 1647 nucleotides
Theoretical weight: 528.13 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

5 bound ligands:
Ligand MG 90 x MG
Ligand K 35 x K
Ligand LMT 1 x LMT
Ligand ATP 1 x ATP
Ligand SF4 1 x SF4
1 modified residue:
Ligand SAC 1 x SAC

Experiments and Validation Details

Entry percentile scores
Resolution: 2.57Å
Relevant EMDB volumes: EMD-16966

Quick links

Citations

1 citations in other articles

Testing a Hypothesis of 12S rRNA Methylation by Putative METTL17 Methyltransferase.
Mashkovskaia et al. (2023)