Structure analysis

Structure of the yeast mitochondrial ribosome - Class A

Electron Microscopy
3.25Å resolution
Source organism: Saccharomyces cerevisiae
Assembly composition:
hetero 78-mer (preferred)
Entry contents: 75 distinct polypeptide molecules
3 distinct RNA molecules

Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 78-mer
PDBe Complex ID: PDB-CPX-126972

Macromolecules

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Chain: D
Length: 252 amino acids
Theoretical weight: 28.25 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P51998 (Residues: 29-280; Coverage: 88%)
Gene names: YML025C, YML6
Pfam: Ribosomal protein L4/L1 family
InterPro:

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Chain: G
Length: 74 amino acids
Theoretical weight: 8.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53724 (Residues: 10-83; Coverage: 53%)
Gene names: MRPL50, N3220, YNR022C
InterPro:

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Chain: M
Length: 151 amino acids
Theoretical weight: 17.18 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25626 (Residues: 16-166; Coverage: 89%)
Gene names: IMG1, PETCR46, YCR046C, YCR46C
Pfam: Ribosomal protein L19
InterPro:

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Chain: N
Length: 118 amino acids
Theoretical weight: 13.51 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40858 (Residues: 44-161; Coverage: 73%)
Gene names: J0904, MRPL49, YJL096W
Pfam: Ribosomal prokaryotic L21 protein
InterPro:

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Chain: O
Length: 225 amino acids
Theoretical weight: 25.96 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53881 (Residues: 85-309; Coverage: 73%)
Gene names: MRPL22, N1657, YNL177C
Pfam: Ribosomal protein L22p/L17e
InterPro:

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Chain: P
Length: 207 amino acids
Theoretical weight: 24.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32387 (Residues: 55-261; Coverage: 79%)
Gene names: D9509.23, MRP20, MRPL41, YDR405W
Pfam: Ribosomal protein L23
InterPro:

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Chain: Q
Length: 296 amino acids
Theoretical weight: 33.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36534 (Residues: 2-297; Coverage: 100%)
Gene names: MRPL40, YPL173W
InterPro:

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Chain: R
Length: 337 amino acids
Theoretical weight: 39.52 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P12687 (Residues: 35-371; Coverage: 91%)
Gene names: MRP7, MRPL2, N2007, YNL005C
Pfam:
InterPro:

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Chain: S
Length: 216 amino acids
Theoretical weight: 25.19 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36525 (Residues: 22-237; Coverage: 84%)
Gene names: MRPL14, MRPL24, YM9646.05, YMR193W
Pfam: Ribosomal L28 family
InterPro:

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Chain: T
Length: 225 amino acids
Theoretical weight: 26.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36517 (Residues: 15-239; Coverage: 71%)
Gene names: L9753.1, MRPL4, YLR439W
Pfam: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
InterPro:

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Chain: V
Length: 177 amino acids
Theoretical weight: 20.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36531 (Residues: 1-177; Coverage: 100%)
Gene names: MRPL36, YBR0918, YBR122C
Pfam: Ribosomal protein L31p, N-terminal
InterPro: Large ribosomal subunit protein bL31m

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Chain: W
Length: 112 amino acids
Theoretical weight: 13.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25348 (Residues: 72-183; Coverage: 61%)
Gene names: MRPL32, YCR003W, YCR041, YCR3W
Pfam: Ribosomal L32p protein family
InterPro:

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Chain: X
Length: 64 amino acids
Theoretical weight: 7.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36533 (Residues: 6-69; Coverage: 91%)
Gene names: MRPL39, YM9571.09C, YML009C
InterPro:

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Chain: Y
Length: 46 amino acids
Theoretical weight: 5.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04598 (Residues: 60-105; Coverage: 44%)
Gene names: YD9727.10, YDR115W
Pfam: Ribosomal protein L34
InterPro: Large ribosomal subunit protein bL34

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Chain: Z
Length: 62 amino acids
Theoretical weight: 7.21 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53921 (Residues: 54-115; Coverage: 54%)
Gene names: MRP35, N1901, YNL122C
Pfam: Ribosomal protein L35
InterPro:

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Chain: 0
Length: 38 amino acids
Theoretical weight: 4.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O14464 (Residues: 56-93; Coverage: 41%)
Gene names: RTC6, TAE4, YPL183BW, YPL183W-A
Pfam: Ribosomal protein L36
InterPro:

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Chain: 1
Length: 348 amino acids
Theoretical weight: 40.7 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06678 (Residues: 20-367; Coverage: 95%)
Gene names: D9798.5, MRPL35, YDR322W
Pfam: Phosphatidylethanolamine-binding protein
InterPro:

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Chain: 2
Length: 113 amino acids
Theoretical weight: 13.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36527 (Residues: 34-146; Coverage: 77%)
Gene names: D8035.6, MRPL28, YDR462W
Pfam: Mitochondrial ribosomal protein L28
InterPro:

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Chain: 3
Length: 130 amino acids
Theoretical weight: 14.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36526 (Residues: 17-146; Coverage: 89%)
Gene names: MRPL27, YBR2019, YBR282W
Pfam: Mitochondrial ribosomal protein L27
InterPro: Large ribosomal subunit protein mL41

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Chain: 4
Length: 138 amino acids
Theoretical weight: 15.91 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06090 (Residues: 2-139; Coverage: 99%)
Gene names: MRPL51, P8283.12, YPR100W
Pfam: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
InterPro:

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Chain: 6
Length: 281 amino acids
Theoretical weight: 32.26 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36528 (Residues: 1-281; Coverage: 100%)
Gene names: MRPL17, MRPL30, N0864, YNL252C
Pfam: 39S mitochondrial ribosomal protein L46
InterPro:

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Chain: 7
Length: 106 amino acids
Theoretical weight: 12.18 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25642 (Residues: 41-146; Coverage: 73%)
Gene names: IMG2, YCR071C, YCR71C
Pfam: Mitochondrial large subunit ribosomal protein (Img2)
InterPro: Large ribosomal subunit protein mL49

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Chain: 8
Length: 264 amino acids
Theoretical weight: 30.32 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02204 (Residues: 1-264; Coverage: 100%)
Gene names: MRPL13, YK105, YKR006C
Pfam: Ribosomal subunit 39S
InterPro:

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Chain: 9
Length: 215 amino acids
Theoretical weight: 23.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36523 (Residues: 29-243; Coverage: 85%)
Gene names: MRPL15, YLR312BW, YLR312W-A
Pfam: Ribonuclease III domain
InterPro:

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Chain: a
Length: 177 amino acids
Theoretical weight: 20.51 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22354 (Residues: 19-195; Coverage: 91%)
Gene names: MRPL20, YKR085C, YKR405
Pfam: Mitochondrial ribosomal protein subunit L20
InterPro: Large ribosomal subunit protein mL58

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Chain: b
Length: 155 amino acids
Theoretical weight: 18.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23369 (Residues: 3-157; Coverage: 99%)
Gene names: MRPL25, YGR076C, YMR26
Pfam: Mitochondrial ribosomal protein mL59
InterPro:

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Chain: c
Length: 119 amino acids
Theoretical weight: 14.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14063 (Residues: 13-131; Coverage: 91%)
Gene names: MRPL31, YKL138C
Pfam: Mitochondrial ribosomal protein L31
InterPro: Large ribosomal subunit protein mL60

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Chain: d
Length: 215 amino acids
Theoretical weight: 25.71 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06630 (Residues: 1-215; Coverage: 95%)
Gene names: MHR1, XTC1, YDR296W
Pfam: Transcriptional regulation of mitochondrial recombination
InterPro: Large ribosomal subunit protein mL67

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Chain: AA
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
InterPro: Small ribosomal subunit protein bS1m-like

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Chain: CC
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)
InterPro: Small ribosomal subunit protein uS3m, fungi

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Chain: DD
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
InterPro:

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Chain: FF
Length: 125 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28778 (Residues: 1-125; Coverage: 95%)
Gene names: MRP17, YKL003C
Pfam: Ribosomal protein S6
InterPro:

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Chain: HH
Length: 154 amino acids
Theoretical weight: 17.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03799 (Residues: 2-155; Coverage: 99%)
Gene names: MRPS8, YM8520.07, YMR158W
Pfam: Ribosomal protein S8
InterPro:

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Chain: JJ
Length: 186 amino acids
Theoretical weight: 21.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03201 (Residues: 16-201; Coverage: 92%)
Gene names: RSM10, YD6888.03, YDR041W
Pfam: Ribosomal protein S10p/S20e
InterPro:

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Chain: KK
Length: 148 amino acids
Theoretical weight: 16.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P42847 (Residues: 70-217; Coverage: 68%)
Gene names: MRPS18, N0397, YNL306W
InterPro:

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Chain: LL
Length: 124 amino acids
Theoretical weight: 13.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53732 (Residues: 29-152; Coverage: 81%)
Gene names: MRPS12, N3298, YNR036C
Pfam: Ribosomal protein S12/S23
InterPro:

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Chain: NN
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
InterPro:

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Chain: OO
Length: 253 amino acids
Theoretical weight: 29.52 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21771 (Residues: 34-286; Coverage: 89%)
Gene names: D9651.3, MRPS28, YDR337W
Pfam: Ribosomal protein S15
InterPro:

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Chain: PP
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02608 (Residues: 2-120; Coverage: 98%)
Gene names: LPA4C, MRPS16, YPL013C
Pfam: Ribosomal protein S16
InterPro:

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Chain: QQ
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
InterPro:

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Chain: RR
Length: 99 amino acids
Theoretical weight: 11.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40033 (Residues: 40-138; Coverage: 72%)
Gene names: RSM18, YER050C
Pfam: Ribosomal protein S18
InterPro:

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Chain: SS
Length: 80 amino acids
Theoretical weight: 9.04 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53733 (Residues: 9-88; Coverage: 88%)
Gene names: N3300, RSM19, YNR037C
Pfam: Ribosomal protein S19
InterPro:

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Chain: TT
Length: 92 amino acids
Theoretical weight: 10.87 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38175 (Residues: 86-177; Coverage: 52%)
Gene names: MRP21, MRP50, YBL0702, YBL090W
Pfam: Ribosomal protein S21
InterPro: Small ribosomal subunit protein bS21

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Chain: UU
Length: 233 amino acids
Theoretical weight: 27.1 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40496 (Residues: 1-233; Coverage: 88%)
Gene names: RSM25, YIL093C
Pfam: Mitochondrial ribosomal protein S25
InterPro: Small ribosomal subunit protein mS23, fungi

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Chain: VV
Length: 233 amino acids
Theoretical weight: 26.74 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P17558 (Residues: 2-234; Coverage: 73%)
Gene names: PET123, YOR158W

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Chain: WW
Length: 401 amino acids
Theoretical weight: 45.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01163 (Residues: 50-450; Coverage: 89%)
Gene names: G2856, RSM23, YGL129C
Pfam: Mitochondrial ribosomal death-associated protein 3
InterPro:

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Chain: XX
Length: 96 amino acids
Theoretical weight: 11.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53305 (Residues: 1-96; Coverage: 87%)
Gene names: RSM27, YGR215W
Pfam: Mitochondrial ribosomal subunit S27
InterPro: Small ribosomal subunit protein mS33

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Chain: YY
Length: 273 amino acids
Theoretical weight: 32.33 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03976 (Residues: 47-319; Coverage: 86%)
Gene names: RSM24, YDR175C
Pfam: Mitochondrial ribosomal subunit protein
InterPro:

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Chain: ZZ
Length: 91 amino acids
Theoretical weight: 10.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O75012 (Residues: 5-95; Coverage: 96%)
Gene names: MRP10, YDL045W-A
Pfam: CHCH domain
InterPro: Small ribosomal subunit protein mS37, fungal-type

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Chain: 11
Length: 34 amino acids
Theoretical weight: 4.38 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32344 (Residues: 78-111; Coverage: 31%)
Gene names: COX24, QRI5, YLR204W
Pfam: Mitochondrial mRNA-processing protein COX24, C-terminal
InterPro: Ribosomal protein mS38, C-terminal

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Chain: 22
Length: 99 amino acids
Theoretical weight: 11.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38783 (Residues: 30-128; Coverage: 76%)
Gene names: FYV4, YHR059W
Pfam: IGR protein motif
InterPro:

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Chain: 44
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
InterPro:

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Chain: 55
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

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Chain: 66
Length: 319 amino acids
Theoretical weight: 36.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53292 (Residues: 27-345; Coverage: 93%)
Gene names: MRPS35, YGR165W
Pfam: Eukaryotic mitochondrial regulator protein
InterPro: Small ribosomal subunit protein mS45

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Chain: 77
Length: 165 amino acids
Theoretical weight: 18.9 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03430 (Residues: 197-361; Coverage: 46%)
Gene names: RSM28, YDR494W

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Chain: 88
Length: 457 amino acids
Theoretical weight: 51.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28817 (Residues: 36-492; Coverage: 91%)
Gene names: EHD3, MRP5, YD9673.08C, YDR036C
Pfam: Enoyl-CoA hydratase/isomerase
InterPro:

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Chain: cc
Length: 94 amino acids
Theoretical weight: 8.02 KDa
Source organism: Saccharomyces cerevisiae

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Chain: dd
Length: 151 amino acids
Theoretical weight: 12.87 KDa
Source organism: Saccharomyces cerevisiae

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Name: 21S ribosomal RNA
Representative chains: A
Length: 3296 nucleotides
Theoretical weight: 1057.79 KDa
Rfam: Bacterial large subunit ribosomal RNA

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Name: 15S ribosomal RNA
Representative chains: aa
Length: 1649 nucleotides
Theoretical weight: 528.78 KDa
Rfam: Bacterial small subunit ribosomal RNA

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Name: tRNA
Representative chains: bb
Length: 76 nucleotides
Theoretical weight: 24.42 KDa
Rfam: tRNA

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