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- PDB-9axu: Non-translating S. pombe ribosome large subunit -

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Basic information

Entry
Database: PDB / ID: 9axu
TitleNon-translating S. pombe ribosome large subunit
Components
  • (Large ribosomal subunit protein ...) x 40
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / Non-translating / 60S / Large subunit / S. pombe / Schizosasccharomyces pombe
Function / homology
Function and homology information


cytosolic large ribosomal subunit assembly / ribonuclease MRP complex / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome / tRNA processing ...cytosolic large ribosomal subunit assembly / ribonuclease MRP complex / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome / tRNA processing / pre-mRNA intronic binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / negative regulation of gene expression / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily ...Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L44e signature. / : / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein L19, eukaryotic / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / : / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L7A/L8 / 60S ribosomal protein L6E / 60S ribosomal protein L35 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal protein L31e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L31e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal protein L35A superfamily / Ribosomal L39 protein / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L14
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL22A ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL19B / Large ribosomal subunit protein eL21B / Large ribosomal subunit protein uL13A / Large ribosomal subunit protein uL30C / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL18B / Large ribosomal subunit protein eL24B / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL6B / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL36B / Large ribosomal subunit protein eL37B / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL14B / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL2C / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein uL3A / Large ribosomal subunit protein eL30A / Large ribosomal subunit protein uL15B / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL32A / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL16A / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL23A / Large ribosomal subunit protein eL18B / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL34B / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL15B / Large ribosomal subunit protein eL38A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL42
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.94 Å
AuthorsGluc, M. / Gemin, O. / Purdy, M. / Mattei, S. / Jomaa, A.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
American Cancer Society United States
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND Germany
CitationJournal: Nat Commun / Year: 2024
Title: Ribosomes hibernate on mitochondria during cellular stress.
Authors: Olivier Gemin / Maciej Gluc / Higor Rosa / Michael Purdy / Moritz Niemann / Yelena Peskova / Simone Mattei / Ahmad Jomaa /
Abstract: Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated ...Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence.
History
DepositionMar 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Large ribosomal subunit protein eL42
1: Large ribosomal subunit protein eL43A
2: 28S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
N: Large ribosomal subunit protein uL2C
O: Large ribosomal subunit protein uL3A
P: Large ribosomal subunit protein uL4A
Q: Large ribosomal subunit protein uL18B
R: Large ribosomal subunit protein eL6
S: Large ribosomal subunit protein uL30C
T: Large ribosomal subunit protein eL8
U: Large ribosomal subunit protein uL6B
V: Large ribosomal subunit protein uL16A
W: Large ribosomal subunit protein uL5A
X: Large ribosomal subunit protein eL13
Y: Large ribosomal subunit protein eL14
Z: Large ribosomal subunit protein eL15B
a: Large ribosomal subunit protein uL13A
b: Large ribosomal subunit protein uL22A
c: Large ribosomal subunit protein eL18B
d: Large ribosomal subunit protein eL19B
e: Large ribosomal subunit protein eL20A
f: Large ribosomal subunit protein eL21B
g: Large ribosomal subunit protein eL22
h: Large ribosomal subunit protein uL14B
i: Large ribosomal subunit protein eL24B
j: Large ribosomal subunit protein uL23A
k: Large ribosomal subunit protein uL24
l: Large ribosomal subunit protein eL27A
m: Large ribosomal subunit protein uL15B
n: Large ribosomal subunit protein eL29
o: Large ribosomal subunit protein eL30A
p: Large ribosomal subunit protein eL31
q: Large ribosomal subunit protein eL32A
r: Large ribosomal subunit protein eL33A
s: Large ribosomal subunit protein eL34B
t: Large ribosomal subunit protein uL29
u: Large ribosomal subunit protein eL36B
v: Large ribosomal subunit protein eL37B
w: Large ribosomal subunit protein eL38A
x: Large ribosomal subunit protein eL39
y: Large ribosomal subunit protein eL28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,009,666143
Polymers2,007,11343
Non-polymers2,554100
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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Large ribosomal subunit protein ... , 40 types, 40 molecules 01NOPQRSTUVWXYZabcdefghijklmno...

#1: Protein Large ribosomal subunit protein eL42


Mass: 12239.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTI8
#2: Protein Large ribosomal subunit protein eL43A / L37A


Mass: 10444.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9HGL8
#6: Protein Large ribosomal subunit protein uL2C / 60S ribosomal protein L2-C / K37 / K5 / KD4


Mass: 27151.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT72
#7: Protein Large ribosomal subunit protein uL3A


Mass: 43889.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P40372
#8: Protein Large ribosomal subunit protein uL4A / 60S ribosomal protein L4-A / L2


Mass: 39839.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P35679
#9: Protein Large ribosomal subunit protein uL18B / 60S ribosomal protein L5-B


Mass: 33538.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74306
#10: Protein Large ribosomal subunit protein eL6


Mass: 21285.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79071
#11: Protein Large ribosomal subunit protein uL30C / 60S ribosomal protein L7-C


Mass: 28780.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O60143
#12: Protein Large ribosomal subunit protein eL8 / L4 / L7A


Mass: 28659.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13672
#13: Protein Large ribosomal subunit protein uL6B / 60S ribosomal protein L9-B


Mass: 21413.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74905
#14: Protein Large ribosomal subunit protein uL16A / QM protein homolog / SpQM


Mass: 25421.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09127
#15: Protein Large ribosomal subunit protein uL5A


Mass: 19928.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT77
#16: Protein Large ribosomal subunit protein eL13


Mass: 23578.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74175
#17: Protein Large ribosomal subunit protein eL14


Mass: 15241.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94238
#18: Protein Large ribosomal subunit protein eL15B / 60S ribosomal protein L15-B / SP-L12


Mass: 23878.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9US22
#19: Protein Large ribosomal subunit protein uL13A / 60S ribosomal protein L16-A


Mass: 22050.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42848
#20: Protein Large ribosomal subunit protein uL22A


Mass: 20854.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14339
#21: Protein Large ribosomal subunit protein eL18B / 60S ribosomal protein L18-B


Mass: 21234.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q8TFH1
#22: Protein Large ribosomal subunit protein eL19B / 60S ribosomal protein L19-B


Mass: 22813.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42699
#23: Protein Large ribosomal subunit protein eL20A / YL17


Mass: 20642.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT68
#24: Protein Large ribosomal subunit protein eL21B / 60S ribosomal protein L21-B


Mass: 18390.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42706
#25: Protein Large ribosomal subunit protein eL22


Mass: 13344.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09668
#26: Protein Large ribosomal subunit protein uL14B / 60S ribosomal protein L23-B


Mass: 14905.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT61
#27: Protein Large ribosomal subunit protein eL24B / 60S ribosomal protein L24-B


Mass: 16957.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74884
#28: Protein Large ribosomal subunit protein uL23A


Mass: 15870.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10330
#29: Protein Large ribosomal subunit protein uL24


Mass: 14375.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P78946
#30: Protein Large ribosomal subunit protein eL27A


Mass: 15421.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14388
#31: Protein Large ribosomal subunit protein uL15B / 60S ribosomal protein L28-B


Mass: 16723.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P57728
#32: Protein Large ribosomal subunit protein eL29 / L43


Mass: 7224.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q92366
#33: Protein Large ribosomal subunit protein eL30A / 60S ribosomal protein L30-1 / L32


Mass: 11610.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P52808
#34: Protein Large ribosomal subunit protein eL31


Mass: 13290.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9URX6
#35: Protein Large ribosomal subunit protein eL32A


Mass: 14491.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79015
#36: Protein Large ribosomal subunit protein eL33A / 60S ribosomal protein L33-A / L37A


Mass: 12212.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USX4
#37: Protein Large ribosomal subunit protein eL34B / 60S ribosomal protein L34-2 / 60S ribosomal protein L34-B


Mass: 12828.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9URT8
#38: Protein Large ribosomal subunit protein uL29


Mass: 14333.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74904
#39: Protein Large ribosomal subunit protein eL36B


Mass: 11287.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94658
#40: Protein Large ribosomal subunit protein eL37B / L37-2 / YL27


Mass: 10112.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05733
#41: Protein Large ribosomal subunit protein eL38A


Mass: 8511.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USR7
#42: Protein Large ribosomal subunit protein eL39 / YL36


Mass: 6326.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05767
#43: Protein Large ribosomal subunit protein eL28 / Probable 60S ribosomal protein L28e


Mass: 14781.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14069

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RNA chain , 3 types, 3 molecules 234

#3: RNA chain 28S ribosomal RNA


Mass: 1129828.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 157310483
#4: RNA chain 5S ribosomal RNA


Mass: 78518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 157310380
#5: RNA chain 5.8S ribosomal RNA


Mass: 52880.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 288694

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Non-polymers , 2 types, 100 molecules

#44: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#45: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 97 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
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

ComponentName: Non-translating S. pombe ribosome large subunit / Type: RIBOSOME / Entity ID: #1-#43 / Source: NATURAL
Molecular weightValue: 3.5 MDa / Experimental value: NO
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)
Buffer solutionpH: 7.4
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 820453 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 37.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0018133233
ELECTRON MICROSCOPYf_angle_d0.5028196871
ELECTRON MICROSCOPYf_chiral_restr0.034224732
ELECTRON MICROSCOPYf_plane_restr0.003612022
ELECTRON MICROSCOPYf_dihedral_angle_d15.221948742

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