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- PDB-9hlz: Translational activators Aep1, Aep2 and Atp25 in complex with mRN... -

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Basic information

Entry
Database: PDB / ID: 9hlz
TitleTranslational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome
Components
  • (ATPase expression protein ...) x 2
  • (Large ribosomal subunit protein ...) x 39
  • (Small ribosomal subunit protein ...) x 34
  • 15S mitochondrial rRNA
  • 21S mitochondrial rRNA
  • ATPase synthesis protein 25, mitochondrial
  • E/E-site formyl-methionine tRNA
KeywordsRIBOSOME / Mitoribosome / translation
Function / homology
Function and homology information


mitochondrial translational initiation / mitochondrial respiratory chain complex IV assembly / mitochondrial ribosome assembly / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / superoxide dismutase activity / mRNA processing / ribosome biogenesis / mitochondrial inner membrane ...mitochondrial translational initiation / mitochondrial respiratory chain complex IV assembly / mitochondrial ribosome assembly / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / superoxide dismutase activity / mRNA processing / ribosome biogenesis / mitochondrial inner membrane / structural constituent of ribosome / mitochondrion / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
54S ribosomal protein L28, mitochondrial / Protein Fyv4 / Small ribosomal subunit protein mS41 SAM domain / IGR protein motif / IGR / : / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal ...54S ribosomal protein L28, mitochondrial / Protein Fyv4 / Small ribosomal subunit protein mS41 SAM domain / IGR protein motif / IGR / : / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / 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 / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Ribosomal protein L36 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36m / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein mL40 / Small ribosomal subunit protein mS41 / Small ribosomal subunit protein mS42 / Large ribosomal subunit protein mL38
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 mS44
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 1
b: ATPase expression protein 2
c: ATPase synthesis protein 25, mitochondrial
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)3,769,714379
Polymers3,761,92379
Non-polymers7,790300
Water00
1


  • Idetical with deposited unit
  • defined by author&software
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


Mass: 36775.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#5: Protein Small ribosomal subunit protein mS44


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


Mass: 39638.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein mS45 / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#7: Protein Small ribosomal subunit protein mS46


Mass: 41281.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#8: Protein Small ribosomal subunit protein mS47


Mass: 56351.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#9: Protein Small ribosomal subunit protein bS1m


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


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


Mass: 47170.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#12: Protein Small ribosomal subunit protein uS4m


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


Mass: 34941.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#14: Protein Small ribosomal subunit protein bS6m


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


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


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


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


Mass: 23458.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#19: Protein Small ribosomal subunit protein uS11m


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


Mass: 16948.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#21: Protein Small ribosomal subunit protein uS13m


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


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


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


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


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


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


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


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


Mass: 30554.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#30: Protein Small ribosomal subunit protein mS29


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


Mass: 12420.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#32: Protein Small ribosomal subunit protein mS35


Mass: 37458.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#33: Protein Small ribosomal subunit protein mS37


Mass: 10709.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#69: Protein Small ribosomal subunit protein mS26


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

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ATPase expression protein ... , 2 types, 2 molecules ab

#34: Protein ATPase expression protein 1


Mass: 59830.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#35: Protein ATPase expression protein 2


Mass: 67632.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)

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Protein , 1 types, 1 molecules c

#36: Protein ATPase synthesis protein 25, mitochondrial


Mass: 70517.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)

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RNA chain , 3 types, 3 molecules tAAr

#37: 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)
#48: 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)
#79: 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...

#38: 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
#39: 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
#40: 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
#41: Protein Large ribosomal subunit protein mL41


Mass: 16521.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#42: Protein Large ribosomal subunit protein mL43


Mass: 16153.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#43: Protein Large ribosomal subunit protein mL44


Mass: 44058.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#44: Protein Large ribosomal subunit protein mL46


Mass: 32261.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#45: Protein Large ribosomal subunit protein mL49


Mass: 16406.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#46: Protein Large ribosomal subunit protein mL50


Mass: 30317.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#47: Protein Large ribosomal subunit protein mL57


Mass: 28206.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#49: Protein Large ribosomal subunit protein uL2m


Mass: 43870.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#50: Protein Large ribosomal subunit protein uL3m


Mass: 29843.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#51: Protein Large ribosomal subunit protein uL4m


Mass: 32014.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#52: Protein Large ribosomal subunit protein uL5m


Mass: 33152.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#53: Protein Large ribosomal subunit protein uL6m


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


Mass: 16313.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#55: Protein Large ribosomal subunit protein uL13m


Mass: 18499.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#56: Protein Large ribosomal subunit protein uL14m


Mass: 14929.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#57: Protein Large ribosomal subunit protein uL15m


Mass: 36414.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#58: Protein Large ribosomal subunit protein uL16m


Mass: 26569.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#59: Protein Large ribosomal subunit protein bL17m


Mass: 26989.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#60: Protein Large ribosomal subunit protein bL19m


Mass: 19428.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#61: Protein Large ribosomal subunit protein bL21m


Mass: 18420.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#62: Protein Large ribosomal subunit protein uL22m


Mass: 34957.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#63: 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)
#64: Protein Large ribosomal subunit protein uL24m


Mass: 33808.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#65: Protein Large ribosomal subunit protein bL27m


Mass: 43310.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#66: Protein Large ribosomal subunit protein bL28m


Mass: 30109.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#67: Protein Large ribosomal subunit protein uL29m


Mass: 37019.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#68: Protein Large ribosomal subunit protein uL30m


Mass: 9549.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#70: Protein Large ribosomal subunit protein bL31m


Mass: 20125.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#71: Protein Large ribosomal subunit protein bL32m


Mass: 21483.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#72: Protein Large ribosomal subunit protein bL33m


Mass: 7992.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#73: Protein Large ribosomal subunit protein bL34m


Mass: 12054.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#74: Protein Large ribosomal subunit protein bL35m


Mass: 13276.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#75: Protein Large ribosomal subunit protein mL58


Mass: 22431.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#76: Protein Large ribosomal subunit protein mL59


Mass: 18626.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#77: Protein Large ribosomal subunit protein mL60


Mass: 15555.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)
#78: Protein Large ribosomal subunit protein mL67


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

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Non-polymers , 2 types, 300 molecules

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


Mass: 24.305 Da / Num. of mol.: 299 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#81: 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
1Aep1, Aep2 and Atp25 in complex with the 74S mitochondrial ribosomeRIBOSOME#1-#790NATURAL
254S mitoribosomal large subunitCOMPLEX#38-#68, #70-#781NATURAL
3Aep1, Aep2 and Atp25 bound to the 37S mitoribosomal small subunitCOMPLEX#1-#36, #69, #791NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Saccharomyces cerevisiae (brewer's yeast)4932W303
32Saccharomyces cerevisiae (brewer's yeast)4932W303
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 holderCryogen: NITROGEN / Specimen 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
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 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 E-site tRNA1PDBexperimental model
28OM4

8om4

8OM4Small subunit2PDBexperimental model
3Aep1, Aep2, Atp25AlphaFoldin silico model

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