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- PDB-8ux4: Mitochondrial ribosome of saccharomyces cerevisiae class II from ... -

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Basic information

Entry
Database: PDB / ID: 8ux4
TitleMitochondrial ribosome of saccharomyces cerevisiae class II from YEP with Dextrose culture
Components
  • (37S ribosomal protein ...) x 2
  • (Large ribosomal subunit protein ...) x 39
  • (Small ribosomal subunit ...) x 31
  • Large ribosomal subunit rRNA
  • MRPL38 isoform 1
  • MRPS9 isoform 1
  • mRNA
KeywordsRIBOSOME / Dextrose treated mitochondrial ribosome
Function / homology
Function and homology information


positive regulation of mitochondrial DNA replication / mitochondrial translational initiation / mitochondrial respiratory chain complex IV assembly / Mitochondrial protein degradation / mitochondrial ribosome assembly / ribonuclease III activity / : / DNA strand exchange activity / mitochondrial large ribosomal subunit / mitochondrial ribosome ...positive regulation of mitochondrial DNA replication / mitochondrial translational initiation / mitochondrial respiratory chain complex IV assembly / Mitochondrial protein degradation / mitochondrial ribosome assembly / ribonuclease III activity / : / DNA strand exchange activity / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / superoxide dismutase activity / RNA processing / cell redox homeostasis / mRNA processing / peroxisome / single-stranded DNA binding / double-stranded RNA binding / 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 / Mitochondrial homologous recombination protein 1 ...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 / Eukaryotic mitochondrial regulator protein / 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 / 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 / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / 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 / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein mS23 / Large ribosomal subunit protein uL29m / Small ribosomal subunit protein bS18m / Large ribosomal subunit protein bL36m / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein mS23 / Large ribosomal subunit protein uL29m / Small ribosomal subunit protein bS18m / 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 / Large ribosomal subunit protein uL3m / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein uL23m / 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 uL5m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein mL57 / 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 / 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 / Small ribosomal subunit protein uS13m / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS10m / 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 / Large ribosomal subunit protein uL13m
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYu, Z. / Zheng, F. / Zhou, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
Citation
Journal: To Be Published
Title: The context-dependent plasticity and polymorphism of yeast mitochondrial ribosome
Authors: Yu, Z. / Zheng, F. / Zhou, C.
#1: Journal: To Be Published
Title: The context-dependent plasticity and polymorphism of yeast mitochondrial ribosome
Authors: Yu, Z. / Zheng, F. / Zhou, C.
History
DepositionNov 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data 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
AA: Small ribosomal subunit protein mS38
AB: Small ribosomal subunit protein mS41
AC: Small ribosomal subunit protein mS42
AD: Small ribosomal subunit protein mS43
AE: Small ribosomal subunit protein mS27
AF: Small ribosomal subunit protein mS45
AG: Small ribosomal subunit protein mS23
AH: Small ribosomal subunit protein mS26
AI: Small ribosomal subunit protein mS29
AJ: Small ribosomal subunit protein mS33
AK: Small ribosomal subunit protein mS35
AL: Small ribosomal subunit rRNA
AM: Small ribosomal subunit tRNA
AN: mRNA
Z: Small ribosomal subunit protein mS37
g: Small ribosomal subunit protein bS1m
h: Small ribosomal subunit protein uS2m
i: Small ribosomal subunit protein uS3m
j: Small ribosomal subunit protein uS4m
k: Small ribosomal subunit protein uS5m
l: 37S ribosomal protein MRP17, mitochondrial
m: Small ribosomal subunit protein uS7m
n: 37S ribosomal protein S8, mitochondrial
o: Small ribosomal subunit protein uS9m
p: Small ribosomal subunit protein uS10m
q: Small ribosomal subunit protein uS11m
r: Small ribosomal subunit protein uS12m
s: Small ribosomal subunit protein uS13m
t: Small ribosomal subunit protein uS14m
u: Small ribosomal subunit protein uS15m
v: Small ribosomal subunit protein bS16m
w: MRPL38 isoform 1
x: Small ribosomal subunit protein bS18m
y: Small ribosomal subunit protein uS19m
z: Small ribosomal subunit protein bS21m
0: Large ribosomal subunit protein bL36m
1: Large ribosomal subunit protein mL38
2: Large ribosomal subunit protein mL40
3: Large ribosomal subunit protein mL41
4: Large ribosomal subunit protein mL43
5: Large ribosomal subunit protein mL44
6: Large ribosomal subunit protein mL46
7: Large ribosomal subunit protein mL49
8: Large ribosomal subunit protein uL30m
9: Large ribosomal subunit protein mL57
A: Large ribosomal subunit rRNA
B: Large ribosomal subunit protein uL2m
C: Large ribosomal subunit protein uL3m
D: Large ribosomal subunit protein uL4m
E: Large ribosomal subunit protein uL5m
F: Large ribosomal subunit protein uL6m
G: Large ribosomal subunit protein bL9m
H: Large ribosomal subunit protein uL13m
I: Large ribosomal subunit protein uL14m
J: Large ribosomal subunit protein uL15m
K: Large ribosomal subunit protein uL16m
L: Large ribosomal subunit protein bL17m
M: Large ribosomal subunit protein bL19m
N: Large ribosomal subunit protein bL21m
O: Large ribosomal subunit protein uL22m
P: Large ribosomal subunit protein uL23m
Q: Large ribosomal subunit protein uL24m
R: Large ribosomal subunit protein bL27m
S: MRPS9 isoform 1
T: Large ribosomal subunit protein uL29m
U: Large ribosomal subunit protein uL30m
V: Large ribosomal subunit protein bL31m
W: Large ribosomal subunit protein bL32m
X: Large ribosomal subunit protein bL33m
Y: Large ribosomal subunit protein bL34m
a: Large ribosomal subunit protein mL58
b: Large ribosomal subunit protein mL59
c: Large ribosomal subunit protein mL60
d: Large ribosomal subunit protein mL67
e: Large ribosomal subunit protein uL10m
f: Large ribosomal subunit protein uL11m


Theoretical massNumber of molelcules
Total (without water)3,013,31476
Polymers3,013,31476
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Small ribosomal subunit ... , 31 types, 31 molecules AAABACADAEAFAGAHAIAJAKALAMZghijkmopqrstuvxyz

#1: Protein/peptide Small ribosomal subunit protein mS38


Mass: 4383.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32344
#2: Protein Small ribosomal subunit protein mS41 / Function required for yeast viability protein 4 / Protein FYV4 / mitochondrial


Mass: 11429.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38783
#3: Protein Small ribosomal subunit protein mS42


Mass: 29423.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47141
#4: Protein Small ribosomal subunit protein mS43 / 37S ribosomal protein MRP1 / mitochondrial


Mass: 34452.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10662
#5: Protein Small ribosomal subunit protein mS27 / 37S ribosomal protein MRP13 / mitochondrial / Small ribosomal subunit protein mS44 / YmS-A


Mass: 34436.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12686
#6: Protein Small ribosomal subunit protein mS45 / 37S ribosomal protein S35 / mitochondrial


Mass: 36902.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53292
#7: Protein Small ribosomal subunit protein mS23


Mass: 27447.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZVI4
#8: Protein Small ribosomal subunit protein mS26


Mass: 26868.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17558
#9: Protein Small ribosomal subunit protein mS29


Mass: 46025.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01163
#10: Protein Small ribosomal subunit protein mS33


Mass: 11030.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53305
#11: Protein Small ribosomal subunit protein mS35 / 37S ribosomal protein S24 / mitochondrial / Mitochondrial ribosomal small subunit protein 24


Mass: 31351.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03976
#12: RNA chain Small ribosomal subunit rRNA


Mass: 480799.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#13: RNA chain Small ribosomal subunit tRNA


Mass: 24422.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#15: Protein Small ribosomal subunit protein mS37 / 37S ribosomal protein MRP10 / mitochondrial / YmS-T


Mass: 10305.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O75012
#16: Protein Small ribosomal subunit protein bS1m / 37S ribosomal protein MRP51 / mitochondrial


Mass: 34118.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02950
#17: Protein Small ribosomal subunit protein uS2m


Mass: 29714.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32902
#18: Protein Small ribosomal subunit protein uS3m / Ribosomal protein VAR1 / mitochondrial


Mass: 38312.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02381
#19: Protein Small ribosomal subunit protein uS4m / 37S ribosomal protein NAM9 / mitochondrial / Nuclear accommodation of mitochondria protein 9


Mass: 56319.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27929
#20: Protein Small ribosomal subunit protein uS5m / 37S ribosomal protein S5 / mitochondrial


Mass: 33240.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33759
#22: Protein Small ribosomal subunit protein uS7m


Mass: 18271.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47150
#24: Protein Small ribosomal subunit protein uS9m / 37S ribosomal protein S9 / mitochondrial


Mass: 27960.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38120
#25: Protein Small ribosomal subunit protein uS10m / 37S ribosomal protein S10 / mitochondrial


Mass: 15701.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03201
#26: Protein Small ribosomal subunit protein uS11m


Mass: 17205.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P42847
#27: Protein Small ribosomal subunit protein uS12m


Mass: 13639.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53732
#28: Protein Small ribosomal subunit protein uS13m


Mass: 13474.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53937
#29: Protein Small ribosomal subunit protein uS14m / 37S ribosomal protein MRP2 / mitochondrial


Mass: 13374.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10663
#30: Protein Small ribosomal subunit protein uS15m


Mass: 29522.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21771
#31: Protein Small ribosomal subunit protein bS16m / 37S ribosomal protein S16 / mitochondrial


Mass: 11813.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02608
#33: Protein Small ribosomal subunit protein bS18m / 37S ribosomal protein RSM18 / mitochondrial


Mass: 11447.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B3LS63
#34: Protein Small ribosomal subunit protein uS19m


Mass: 9037.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53733
#35: Protein Small ribosomal subunit protein bS21m


Mass: 10872.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38175

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RNA chain , 2 types, 2 molecules ANA

#14: RNA chain mRNA


Mass: 4084.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#46: RNA chain Large ribosomal subunit rRNA


Mass: 923942.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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37S ribosomal protein ... , 2 types, 2 molecules ln

#21: Protein 37S ribosomal protein MRP17, mitochondrial / Mitochondrial small ribosomal subunit protein bS6m / YmS16


Mass: 15046.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P28778
#23: Protein 37S ribosomal protein S8, mitochondrial / Mitochondrial small ribosomal subunit protein uS8m


Mass: 17496.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03799

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Protein , 2 types, 2 molecules wS

#32: Protein MRPL38 isoform 1


Mass: 24012.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#64: Protein MRPS9 isoform 1


Mass: 21885.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Large ribosomal subunit protein ... , 39 types, 39 molecules 0123456789BCDEFGHIJKLMNOPQRTUV...

#36: Protein/peptide Large ribosomal subunit protein bL36m


Mass: 4653.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O14464
#37: Protein Large ribosomal subunit protein mL38


Mass: 40703.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06678
#38: Protein Large ribosomal subunit protein mL40


Mass: 13464.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36527
#39: Protein Large ribosomal subunit protein mL41


Mass: 14841.158 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


Mass: 15909.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06090
#41: Protein Large ribosomal subunit protein mL44


Mass: 36326.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36516
#42: Protein Large ribosomal subunit protein mL46 / 54S ribosomal protein L17 / mitochondrial / YmL17/YmL30


Mass: 30044.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36528
#43: Protein Large ribosomal subunit protein mL49


Mass: 12182.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25642
#44: Protein Large ribosomal subunit protein uL30m


Mass: 23155.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#45: Protein Large ribosomal subunit protein mL57 / 54S ribosomal protein L15 / mitochondrial / YmL15


Mass: 23816.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36523
#47: Protein Large ribosomal subunit protein uL2m / 54S ribosomal protein RML2 / mitochondrial / L2


Mass: 36690.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32611
#48: Protein Large ribosomal subunit protein uL3m


Mass: 27528.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P31334
#49: Protein Large ribosomal subunit protein uL4m / 54S ribosomal protein YmL6 / mitochondrial


Mass: 28254.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P51998
#50: Protein Large ribosomal subunit protein uL5m


Mass: 31014.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36519
#51: Protein Large ribosomal subunit protein uL6m


Mass: 21690.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32904
#52: Protein Large ribosomal subunit protein bL9m


Mass: 8763.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53724
#53: Protein Large ribosomal subunit protein uL13m


Mass: 18125.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's 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 (brewer's yeast) / References: UniProt: P35996
#55: Protein Large ribosomal subunit protein uL15m


Mass: 24765.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36520
#56: Protein Large ribosomal subunit protein uL16m


Mass: 22347.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38064
#57: Protein Large ribosomal subunit protein bL17m / 54S ribosomal protein L8 / mitochondrial / YmL8


Mass: 26858.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22353
#58: Protein Large ribosomal subunit protein bL19m


Mass: 17179.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25626
#59: Protein Large ribosomal subunit protein bL21m


Mass: 13507.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40858
#60: Protein Large ribosomal subunit protein uL22m


Mass: 25964.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53881
#61: Protein Large ribosomal subunit protein uL23m


Mass: 24529.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32387
#62: Protein Large ribosomal subunit protein uL24m / 54S ribosomal protein L40 / mitochondrial / YmL40


Mass: 33676.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36534
#63: Protein Large ribosomal subunit protein bL27m / 54S ribosomal protein L2 / mitochondrial / YMR6 / YmL2


Mass: 39516.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12687
#65: Protein Large ribosomal subunit protein uL29m / 54S ribosomal protein L4 / mitochondrial / YmL4


Mass: 26410.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A7A1V9
#66: Protein Large ribosomal subunit protein uL30m


Mass: 9088.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20084
#67: Protein Large ribosomal subunit protein bL31m / 54S ribosomal protein L36 / mitochondrial / YmL36


Mass: 8754.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36531
#68: Protein Large ribosomal subunit protein bL32m


Mass: 13409.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25348
#69: Protein Large ribosomal subunit protein bL33m


Mass: 7275.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36533
#70: Protein/peptide Large ribosomal subunit protein bL34m


Mass: 5465.526 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04598
#71: Protein Large ribosomal subunit protein mL58


Mass: 20507.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22354
#72: Protein Large ribosomal subunit protein mL59


Mass: 18408.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23369
#73: Protein Large ribosomal subunit protein mL60


Mass: 14277.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14063
#74: Protein Large ribosomal subunit protein mL67 / Cross-linked transcription component 1 / Mitochondrial homologous recombination protein 1


Mass: 25712.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06630
#75: Protein Large ribosomal subunit protein uL10m / 54S ribosomal protein L11 / mitochondrial / YmL11


Mass: 19078.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36521
#76: Protein Large ribosomal subunit protein uL11m


Mass: 14713.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Details

Has ligand of interestN
Has protein modificationN

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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

ComponentName: Mitochondrial ribosome Class II of saccharomyces cerevisiae cultured in YEP with Dextrose
Type: RIBOSOME / Entity ID: #1-#75 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14356 / Symmetry type: POINT

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