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

Electron Microscopy
2.57Å resolution
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
Assembly composition:
hetero 35-mer (preferred)
Entry contents: 34 distinct polypeptide molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 35-mer
Accessible surface area: 481024.61 Å2
Buried surface area: 276513.37 Å2
Dissociation area: 1,880.94 Å2
Dissociation energy (ΔGdiss): 1.28 kcal/mol
Dissociation entropy (TΔSdiss): 15.95 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-238631

Macromolecules

Small ribosomal subunit protein bS1m
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
Pfam: Mitochondrial ribosomal protein subunit
Small ribosomal subunit protein bS1m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein bS1m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein bS1m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS2m
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
Pfam: Ribosomal protein S2
Small ribosomal subunit protein uS2m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS2m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS2m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS3m
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
Pfam: Mitochondrial ribosomal protein (VAR1)
Small ribosomal subunit protein uS3m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS3m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS3m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS4m
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
Pfam: S4 domain
Small ribosomal subunit protein uS4m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS4m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS4m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS5m
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
Pfam:
Small ribosomal subunit protein uS5m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS5m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS5m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein bS6m
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
Pfam: Ribosomal protein S6
Small ribosomal subunit protein bS6m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein bS6m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein bS6m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS7m
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
Pfam: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS7m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS7m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS7m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS8m
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
Pfam: Ribosomal protein S8
Small ribosomal subunit protein uS8m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS8m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS8m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS9m
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
Pfam: Ribosomal protein S9/S16
Small ribosomal subunit protein uS9m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS9m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS9m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS10m
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
Pfam: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS10m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS10m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS10m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS11m
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 uS11m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS11m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS11m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS12m
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
Pfam: Ribosomal protein S12/S23
Small ribosomal subunit protein uS12m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS12m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS12m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS13m
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
Pfam: Ribosomal protein S13/S18
Small ribosomal subunit protein uS13m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS13m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS13m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS14m
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
Pfam: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS14m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS14m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS14m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS15m
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
Pfam: Ribosomal protein S15
Small ribosomal subunit protein uS15m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS15m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS15m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein bS16m
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
Pfam: Ribosomal protein S16
Small ribosomal subunit protein bS16m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein bS16m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein bS16m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS17m
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
Pfam: Ribosomal protein S17
Small ribosomal subunit protein uS17m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS17m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS17m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein bS18m
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
Pfam: Ribosomal protein S18
Small ribosomal subunit protein bS18m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein bS18m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein bS18m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein uS19m
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
Pfam: Ribosomal protein S19
Small ribosomal subunit protein uS19m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein uS19m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein uS19m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein bS21m
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
Pfam: Ribosomal protein S21
Small ribosomal subunit protein bS21m in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein bS21m in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein bS21m in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS23
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
Pfam: Mitochondrial ribosomal protein S25
Small ribosomal subunit protein mS23 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS23 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS23 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS26
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 mS26 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS26 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS26 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS29
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
Pfam: Mitochondrial ribosomal death-associated protein 3
Small ribosomal subunit protein mS29 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS29 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS29 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS33
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
Pfam: Mitochondrial ribosomal subunit S27
Small ribosomal subunit protein mS33 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS33 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS33 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS35
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
Pfam: Mitochondrial ribosomal subunit protein
Small ribosomal subunit protein mS35 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS35 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS35 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS37
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
Pfam: CHCH domain
Small ribosomal subunit protein mS37 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS37 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS37 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS38
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
Pfam: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein mS38 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS38 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS38 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS41
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
Pfam: IGR protein motif
Small ribosomal subunit protein mS41 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS41 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS41 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS42
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
Pfam: Iron/manganese superoxide dismutases, C-terminal domain
Small ribosomal subunit protein mS42 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS42 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS42 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS43
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 mS43 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS43 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS43 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS27
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 mS27 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS27 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS27 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS45
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
Pfam: Eukaryotic mitochondrial regulator protein
Small ribosomal subunit protein mS45 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS45 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS45 in PDB entry 8om2, assembly 1, top view.
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Small ribosomal subunit protein mS47
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
Pfam: Enoyl-CoA hydratase/isomerase
Small ribosomal subunit protein mS47 in PDB entry 8om2, assembly 1, front view.
Small ribosomal subunit protein mS47 in PDB entry 8om2, assembly 1, side view.
Small ribosomal subunit protein mS47 in PDB entry 8om2, assembly 1, top view.
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Ribosome assembly protein RSM22, mitochondrial
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
Pfam: Mitochondrial small ribosomal subunit Rsm22
Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial in PDB entry 8om2, assembly 1, front view.
Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial in PDB entry 8om2, assembly 1, side view.
Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial in PDB entry 8om2, assembly 1, top view.
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RNA chain r
Name: 15S mitochondrial rRNA
Representative chains: r
Length: 1647 nucleotides
Theoretical weight: 528.13 KDa
Rfam: Bacterial small subunit ribosomal RNA
15S mitochondrial rRNA in PDB entry 8om2, assembly 1, front view.
15S mitochondrial rRNA in PDB entry 8om2, assembly 1, side view.
15S mitochondrial rRNA in PDB entry 8om2, assembly 1, top view.
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