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- PDB-9hm0: Translational activator Aep3 in complex with mRNA and the yeast m... -

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Basic information

Entry
Database: PDB / ID: 9hm0
TitleTranslational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome
Components
  • (Large ribosomal subunit protein ...) x 39
  • (Small ribosomal subunit protein ...) x 34
  • 15S mitochondrial rRNA
  • 21S mitochondrial rRNA
  • ATPase expression protein 3
  • E/E-site formyl-methionine tRNA
KeywordsRIBOSOME / Mitoribosome / translation
Function / homology
Function and homology information


Branched-chain amino acid catabolism / positive regulation of mitochondrial DNA replication / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mRNA metabolic process / mitochondrial translational initiation / L-valine catabolic process / mitochondrial respiratory chain complex IV assembly / Mitochondrial protein degradation / mitochondrial ribosome assembly ...Branched-chain amino acid catabolism / positive regulation of mitochondrial DNA replication / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mRNA metabolic process / mitochondrial translational initiation / L-valine catabolic process / mitochondrial respiratory chain complex IV assembly / Mitochondrial protein degradation / mitochondrial ribosome assembly / DNA strand exchange activity / ribonuclease III activity / : / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / sporulation resulting in formation of a cellular spore / superoxide dismutase activity / RNA processing / cell redox homeostasis / mRNA processing / peroxisome / single-stranded DNA binding / double-stranded RNA binding / large ribosomal subunit / ribosome biogenesis / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cellular response to oxidative stress / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / DNA recombination / cytosolic large ribosomal subunit / negative regulation of translation / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / ribosome / translation / mRNA binding / regulation of DNA-templated transcription / GTP binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / 54S ribosomal protein L8, C-terminal / Ribosomal L27 protein, C-terminal / Ribosomal L27 protein C-terminal domain / 54S ribosomal protein L8 C-terminal domain / Large ribosomal subunit protein uL24m / Ribosomal protein VAR1 / Mitochondrial ribosomal protein (VAR1) / Ribosomal protein L31, mitochondrial / Ribosomal protein L20, mitochondrial ...: / 54S ribosomal protein L8, C-terminal / Ribosomal L27 protein, C-terminal / Ribosomal L27 protein C-terminal domain / 54S ribosomal protein L8 C-terminal domain / Large ribosomal subunit protein uL24m / Ribosomal protein VAR1 / Mitochondrial ribosomal protein (VAR1) / Ribosomal protein L31, mitochondrial / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L3, double-stranded RNA binding domain / Mitochondrial ribosomal protein subunit L20 / Transcriptional regulation of mitochondrial recombination / Mitochondrial ribosomal protein mL59 / Mitochondrial ribosomal protein L31 / 54S ribosomal protein L36, yeast / 54S ribosomal protein L28, mitochondrial / : / : / : / Ribosomal protein L31p, N-terminal / Mitochondrial ribosomal protein MRP51, fungi / Mitochondrial ribosomal protein S25 / Ribosomal protein S24, mitochondrial / Ribosomal protein S23, mitochondrial, fungi / Mitochondrial ribosomal protein subunit / Mitochondrial ribosomal protein S25 / Ribosomal protein S35, mitochondrial / Ribosomal protein MRP10, mitochondrial / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / Small ribosomal subunit protein mS41 SAM domain / IGR protein motif / IGR / Ribonuclease-III-like / Ribonuclease III domain / Ribonuclease III family domain profile. / : / Ribonuclease III family / Ribonuclease III domain / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ClpP/crotonase-like domain superfamily / Ribosomal protein S21
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36m / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS43 / Small ribosomal subunit protein uS14m ...GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36m / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS43 / Small ribosomal subunit protein uS14m / Small ribosomal subunit protein mS27 / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein mL60 / Small ribosomal subunit protein mS26 / Large ribosomal subunit protein uL30m / Small ribosomal subunit protein uS15m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL58 / Large ribosomal subunit protein mL59 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein mL49 / Small ribosomal subunit protein uS4m / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein mS47 / Large ribosomal subunit protein uL3m / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein uL2m / Small ribosomal subunit protein uS2m / Large ribosomal subunit protein uL6m / Small ribosomal subunit protein uS5m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL5m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein mL57 / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein bL31m / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein mS41 / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS23 / Large ribosomal subunit protein bL21m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein mS42 / Small ribosomal subunit protein uS7m / Large ribosomal subunit protein uL4m / Small ribosomal subunit protein mS45 / Small ribosomal subunit protein mS33 / Large ribosomal subunit protein bL9m / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS19m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein bL35m / Small ribosomal subunit protein uS13m / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein mL50 / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein mS46 / Small ribosomal subunit protein uS8m / Small ribosomal subunit protein mS35 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL67 / Large ribosomal subunit protein mL38 / ATPase expression protein 3 / Large ribosomal subunit protein uL13m
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsCarlstrom, A. / Rovsnik, U. / Ott, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation.
Authors: Joseph B Bridgers / Andreas Carlström / Dawafuti Sherpa / Mary T Couvillion / Urška Rovšnik / Jingjing Gao / Bowen Wan / Sichen Shao / Martin Ott / L Stirling Churchman /
Abstract: Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains ...Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In Saccharomyces cerevisiae, nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats using selective mitoribosome profiling and cryo-electron microscopy (cryo-EM) structural analysis. These analyses show that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicate that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to mitoribosomes stalled in the post-initiation, pre-elongation state revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5' untranslated region of the client mRNA and the mRNA channel exit to align the mRNA in the small subunit during initiation. Our findings provide a mechanistic basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position mitoribosomes at start codons.
History
DepositionDec 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Small ribosomal subunit protein mS38
2: Small ribosomal subunit protein mS41
3: Small ribosomal subunit protein mS42
4: Small ribosomal subunit protein mS43
5: Small ribosomal subunit protein mS27
6: Small ribosomal subunit protein mS45
7: Small ribosomal subunit protein mS46
8: Small ribosomal subunit protein mS47
A: Small ribosomal subunit protein bS1m
B: Small ribosomal subunit protein uS2m
C: Small ribosomal subunit protein uS3m
D: Small ribosomal subunit protein uS4m
E: Small ribosomal subunit protein uS5m
F: Small ribosomal subunit protein bS6m
G: Small ribosomal subunit protein uS7m
H: Small ribosomal subunit protein uS8m
I: Small ribosomal subunit protein uS9m
J: Small ribosomal subunit protein uS10m
K: Small ribosomal subunit protein uS11m
L: Small ribosomal subunit protein uS12m
M: Small ribosomal subunit protein uS13m
N: Small ribosomal subunit protein uS14m
O: Small ribosomal subunit protein uS15m
P: Small ribosomal subunit protein bS16m
Q: Small ribosomal subunit protein uS17m
R: Small ribosomal subunit protein bS18m
S: Small ribosomal subunit protein uS19m
T: Small ribosomal subunit protein bS21m
U: Small ribosomal subunit protein mS23
W: Small ribosomal subunit protein mS29
X: Small ribosomal subunit protein mS33
Y: Small ribosomal subunit protein mS35
Z: Small ribosomal subunit protein mS37
a: ATPase expression protein 3
t: E/E-site formyl-methionine tRNA
00: Large ribosomal subunit protein bL36m
11: Large ribosomal subunit protein mL38
22: Large ribosomal subunit protein mL40
33: Large ribosomal subunit protein mL41
44: Large ribosomal subunit protein mL43
55: Large ribosomal subunit protein mL44
66: Large ribosomal subunit protein mL46
77: Large ribosomal subunit protein mL49
88: Large ribosomal subunit protein mL50
99: Large ribosomal subunit protein mL57
AA: 21S mitochondrial rRNA
BB: Large ribosomal subunit protein uL2m
CC: Large ribosomal subunit protein uL3m
DD: Large ribosomal subunit protein uL4m
EE: Large ribosomal subunit protein uL5m
FF: Large ribosomal subunit protein uL6m
GG: Large ribosomal subunit protein bL9m
HH: Large ribosomal subunit protein uL13m
II: Large ribosomal subunit protein uL14m
JJ: Large ribosomal subunit protein uL15m
KK: Large ribosomal subunit protein uL16m
LL: Large ribosomal subunit protein bL17m
MM: Large ribosomal subunit protein bL19m
NN: Large ribosomal subunit protein bL21m
OO: Large ribosomal subunit protein uL22m
PP: Large ribosomal subunit protein uL23m
QQ: Large ribosomal subunit protein uL24m
RR: Large ribosomal subunit protein bL27m
SS: Large ribosomal subunit protein bL28m
TT: Large ribosomal subunit protein uL29m
UU: Large ribosomal subunit protein uL30m
V: Small ribosomal subunit protein mS26
VV: Large ribosomal subunit protein bL31m
WW: Large ribosomal subunit protein bL32m
XX: Large ribosomal subunit protein bL33m
YY: Large ribosomal subunit protein bL34m
ZZ: Large ribosomal subunit protein bL35m
aa: Large ribosomal subunit protein mL58
bb: Large ribosomal subunit protein mL59
cc: Large ribosomal subunit protein mL60
dd: Large ribosomal subunit protein mL67
r: 15S mitochondrial rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,642,596395
Polymers3,634,36877
Non-polymers8,228318
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Small ribosomal subunit protein ... , 34 types, 34 molecules 12345678ABCDEFGHIJKLMNOPQRSTUW...

#1: Protein Small ribosomal subunit protein mS38 / Mitochondrial mRNA-processing protein COX24


Mass: 12800.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P32344
#2: Protein Small ribosomal subunit protein mS41 / Function required for yeast viability protein 4 / Protein FYV4 / mitochondrial


Mass: 15321.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P38783
#3: Protein Small ribosomal subunit protein mS42 / 37S ribosomal protein S26 / mitochondrial


Mass: 30257.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P47141
#4: Protein Small ribosomal subunit protein mS43 / 37S ribosomal protein MRP1 / mitochondrial


Mass: 36775.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P10662
#5: Protein Small ribosomal subunit protein mS27 / 37S ribosomal protein MRP13 / mitochondrial / Small ribosomal subunit protein mS44 / YmS-A


Mass: 39045.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P12686
#6: Protein Small ribosomal subunit protein mS45 / 37S ribosomal protein S35 / mitochondrial


Mass: 39638.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53292
#7: Protein Small ribosomal subunit protein mS46 / 37S ribosomal protein RSM28 / mitochondrial


Mass: 41281.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q03430
#8: Protein Small ribosomal subunit protein mS47 / 3-hydroxyisobutyryl-CoA hydrolase / mitochondrial / 3-hydroxyisobutyryl-coenzyme A hydrolase / HIB- ...3-hydroxyisobutyryl-CoA hydrolase / mitochondrial / 3-hydroxyisobutyryl-coenzyme A hydrolase / HIB-CoA hydrolase / HIBYL-CoA-H


Mass: 56351.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
References: UniProt: P28817, 3-hydroxyisobutyryl-CoA hydrolase
#9: Protein Small ribosomal subunit protein bS1m / 37S ribosomal protein MRP51 / mitochondrial


Mass: 39507.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q02950
#10: Protein Small ribosomal subunit protein uS2m / 37S ribosomal protein MRP4 / mitochondrial


Mass: 44205.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P32902
#11: Protein Small ribosomal subunit protein uS3m / Ribosomal protein VAR1 / mitochondrial


Mass: 47170.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P02381
#12: Protein Small ribosomal subunit protein uS4m / 37S ribosomal protein NAM9 / mitochondrial / Nuclear accommodation of mitochondria protein 9


Mass: 56450.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P27929
#13: Protein Small ribosomal subunit protein uS5m / 37S ribosomal protein S5 / mitochondrial


Mass: 34941.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P33759
#14: Protein Small ribosomal subunit protein bS6m / 37S ribosomal protein MRP17 / mitochondrial / YmS16


Mass: 15046.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P28778
#15: Protein Small ribosomal subunit protein uS7m / 37S ribosomal protein S7 / mitochondrial


Mass: 27857.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P47150
#16: Protein Small ribosomal subunit protein uS8m / 37S ribosomal protein S8 / mitochondrial


Mass: 17496.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q03799
#17: Protein Small ribosomal subunit protein uS9m / 37S ribosomal protein S9 / mitochondrial


Mass: 31980.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P38120
#18: Protein Small ribosomal subunit protein uS10m / 37S ribosomal protein S10 / mitochondrial


Mass: 23458.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q03201
#19: Protein Small ribosomal subunit protein uS11m / 37S ribosomal protein S18 / mitochondrial / YmS18


Mass: 24603.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P42847
#20: Protein Small ribosomal subunit protein uS12m / 37S ribosomal protein S12 / mitochondrial


Mass: 16948.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53732
#21: Protein Small ribosomal subunit protein uS13m / 37S ribosomal protein SWS2 / mitochondrial / Sick without securin protein 2


Mass: 16087.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53937
#22: Protein Small ribosomal subunit protein uS14m / 37S ribosomal protein MRP2 / mitochondrial


Mass: 13563.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P10663
#23: Protein Small ribosomal subunit protein uS15m / 37S ribosomal protein S28 / mitochondrial


Mass: 33116.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P21771
#24: Protein Small ribosomal subunit protein bS16m / 37S ribosomal protein S16 / mitochondrial


Mass: 13663.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q02608
#25: Protein Small ribosomal subunit protein uS17m / 37S ribosomal protein S17 / mitochondrial


Mass: 27683.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q03246
#26: Protein Small ribosomal subunit protein bS18m / 37S ribosomal protein RSM18 / mitochondrial


Mass: 15866.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P40033
#27: Protein Small ribosomal subunit protein uS19m / 37S ribosomal protein S19 / mitochondrial


Mass: 10292.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53733
#28: Protein Small ribosomal subunit protein bS21m / 37S ribosomal protein MRP21 / mitochondrial


Mass: 20432.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P38175
#29: Protein Small ribosomal subunit protein mS23 / 37S ribosomal protein S25 / mitochondrial


Mass: 30554.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P40496
#30: Protein Small ribosomal subunit protein mS29 / 37S ribosomal protein S23 / mitochondrial / DAP-3


Mass: 50940.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q01163
#31: Protein Small ribosomal subunit protein mS33 / Mitochondrial 37S ribosomal protein S27


Mass: 12420.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53305
#32: Protein Small ribosomal subunit protein mS35 / 37S ribosomal protein S24 / mitochondrial / Mitochondrial ribosomal small subunit protein 24


Mass: 37458.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q03976
#33: Protein Small ribosomal subunit protein mS37 / 37S ribosomal protein MRP10 / mitochondrial / YmS-T


Mass: 10709.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: O75012
#67: Protein Small ribosomal subunit protein mS26 / 37S ribosomal protein PET123 / mitochondrial


Mass: 36059.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P17558

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Protein , 1 types, 1 molecules a

#34: Protein ATPase expression protein 3


Mass: 70425.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q12089

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RNA chain , 3 types, 3 molecules tAAr

#35: RNA chain E/E-site formyl-methionine tRNA


Mass: 24234.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#46: RNA chain 21S mitochondrial rRNA


Mass: 1057805.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#77: RNA chain 15S mitochondrial rRNA


Mass: 528784.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)

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Large ribosomal subunit protein ... , 39 types, 39 molecules 00112233445566778899BBCCDDEEFFGGHHIIJJKKLLMMNNOOPPQQRRSSTTUU...

#36: Protein Large ribosomal subunit protein bL36m / 54S ribosomal protein RTC6 / mitochondrial / Restriction of telomere capping protein 6 / ...54S ribosomal protein RTC6 / mitochondrial / Restriction of telomere capping protein 6 / Translation associated element 4


Mass: 10718.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: O14464
#37: Protein Large ribosomal subunit protein mL38 / 54S ribosomal protein L35 / mitochondrial / YmL35


Mass: 42886.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q06678
#38: Protein Large ribosomal subunit protein mL40 / 54S ribosomal protein L28 / mitochondrial / YmL28


Mass: 17373.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36527
#39: Protein Large ribosomal subunit protein mL41 / 54S ribosomal protein L27 / mitochondrial / YmL27


Mass: 16521.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36526
#40: Protein Large ribosomal subunit protein mL43 / 54S ribosomal protein L51 / mitochondrial


Mass: 16153.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q06090
#41: Protein Large ribosomal subunit protein mL44 / 54S ribosomal protein L3 / mitochondrial / YmL3


Mass: 44058.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36516
#42: Protein Large ribosomal subunit protein mL46 / 54S ribosomal protein L17 / mitochondrial / YmL17/YmL30


Mass: 32261.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36528
#43: Protein Large ribosomal subunit protein mL49 / 54S ribosomal protein IMG2 / mitochondrial / Integrity of mitochondrial genome protein 2


Mass: 16406.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P25642
#44: Protein Large ribosomal subunit protein mL50 / 54S ribosomal protein L13 / mitochondrial / YmL13


Mass: 30317.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q02204
#45: Protein Large ribosomal subunit protein mL57 / 54S ribosomal protein L15 / mitochondrial / YmL15


Mass: 28206.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36523
#47: Protein Large ribosomal subunit protein uL2m / 54S ribosomal protein RML2 / mitochondrial / L2


Mass: 43870.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P32611
#48: Protein Large ribosomal subunit protein uL3m / 54S ribosomal protein L9 / mitochondrial / YmL9


Mass: 29843.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P31334
#49: Protein Large ribosomal subunit protein uL4m / 54S ribosomal protein YmL6 / mitochondrial


Mass: 32014.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P51998
#50: Protein Large ribosomal subunit protein uL5m / 54S ribosomal protein L7 / mitochondrial / YmL5 / YmL7


Mass: 33152.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36519
#51: Protein Large ribosomal subunit protein uL6m / 54S ribosomal protein L6 / mitochondrial / YmL16


Mass: 23926.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P32904
#52: Protein Large ribosomal subunit protein bL9m / 54S ribosomal protein L50 / mitochondrial


Mass: 16313.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53724
#53: Protein Large ribosomal subunit protein uL13m / 54S ribosomal protein L23 / mitochondrial / YmL23


Mass: 18499.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q12487
#54: Protein Large ribosomal subunit protein uL14m / 54S ribosomal protein L38 / mitochondrial / YmL38


Mass: 14929.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P35996
#55: Protein Large ribosomal subunit protein uL15m / 54S ribosomal protein L10 / mitochondrial / YmL10/YmL18


Mass: 36414.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36520
#56: Protein Large ribosomal subunit protein uL16m / 54S ribosomal protein L16 / mitochondrial / YmL47


Mass: 26569.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P38064
#57: Protein Large ribosomal subunit protein bL17m / 54S ribosomal protein L8 / mitochondrial / YmL8


Mass: 26989.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P22353
#58: Protein Large ribosomal subunit protein bL19m / 54S ribosomal protein IMG1 / mitochondrial / Integrity of mitochondrial genome protein 1 / PetCR46


Mass: 19428.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P25626
#59: Protein Large ribosomal subunit protein bL21m / 54S ribosomal protein L49 / mitochondrial / YmL49


Mass: 18420.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P40858
#60: Protein Large ribosomal subunit protein uL22m / 54S ribosomal protein L22 / mitochondrial


Mass: 34957.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53881
#61: Protein Large ribosomal subunit protein uL23m


Mass: 30616.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#62: Protein Large ribosomal subunit protein uL24m / 54S ribosomal protein L40 / mitochondrial / YmL40


Mass: 33808.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36534
#63: Protein Large ribosomal subunit protein bL27m / 54S ribosomal protein L2 / mitochondrial / YMR6 / YmL2


Mass: 43310.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P12687
#64: Protein Large ribosomal subunit protein bL28m / 54S ribosomal protein L24 / mitochondrial / YmL14/YmL24


Mass: 30109.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36525
#65: Protein Large ribosomal subunit protein uL29m / 54S ribosomal protein L4 / mitochondrial / YmL4


Mass: 37019.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36517
#66: Protein Large ribosomal subunit protein uL30m / 54S ribosomal protein L33 / mitochondrial / YmL33


Mass: 9549.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P20084
#68: Protein Large ribosomal subunit protein bL31m / 54S ribosomal protein L36 / mitochondrial / YmL36


Mass: 20125.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36531
#69: Protein Large ribosomal subunit protein bL32m / 54S ribosomal protein L32 / mitochondrial / YmL32


Mass: 21483.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P25348
#70: Protein Large ribosomal subunit protein bL33m / 54S ribosomal protein L39 / mitochondrial / YmL39


Mass: 7992.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36533
#71: Protein Large ribosomal subunit protein bL34m / 54S ribosomal protein L34 / mitochondrial / L34mt


Mass: 12054.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q04598
#72: Protein Large ribosomal subunit protein bL35m / 54S ribosomal protein MRP35


Mass: 13276.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53921
#73: Protein Large ribosomal subunit protein mL58 / 54S ribosomal protein L20 / mitochondrial / YmL20


Mass: 22431.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P22354
#74: Protein Large ribosomal subunit protein mL59 / 54S ribosomal protein L25 / mitochondrial / YmL25


Mass: 18626.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P23369
#75: Protein Large ribosomal subunit protein mL60 / 54S ribosomal protein L31 / mitochondrial / YmL31


Mass: 15555.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P14063
#76: Protein Large ribosomal subunit protein mL67 / Cross-linked transcription component 1 / Mitochondrial homologous recombination protein 1


Mass: 26937.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q06630

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Non-polymers , 2 types, 318 molecules

#78: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 317 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#79: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Aep3 in complex with the 74S mitochondrial ribosomeRIBOSOME#1-#770NATURAL
237S mitochondrial ribosome small subunitCOMPLEX#1-#33, #67, #771NATURAL
354S mitochondrial ribosome large subunitCOMPLEX#36-#66, #68-#761NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Saccharomyces cerevisiae (brewer's yeast)4932W303
32Saccharomyces cerevisiae (brewer's yeast)4932
43Saccharomyces cerevisiae (brewer's yeast)4932W303
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 400 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207:model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22558 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeDetailsInitial refinement model-IDSource nameType
15MRC

5mrc

5MRCLarge subunit and tRNA in E-site1PDBexperimental model
28OM4

8om4

8OM4Small subunit2PDBexperimental model
3Aep3AlphaFoldin silico model

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