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- PDB-9axt: Non-translating S. pombe ribosome -

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Basic information

Entry
Database: PDB / ID: 9axt
TitleNon-translating S. pombe ribosome
Components
  • (Large ribosomal subunit protein ...) x 40
  • (Small ribosomal subunit protein ...) x 31
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / Schizosaccharomyces pombe / protein synthesis / S. pombe / TRANSLATION
Function / homology
Function and homology information


mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Protein methylation / Protein hydroxylation / RMTs methylate histone arginines / positive regulation of SREBP signaling pathway / Major pathway of rRNA processing in the nucleolus and cytosol / cytosolic large ribosomal subunit assembly ...mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Protein methylation / Protein hydroxylation / RMTs methylate histone arginines / positive regulation of SREBP signaling pathway / Major pathway of rRNA processing in the nucleolus and cytosol / 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) / cytoplasmic translational elongation / preribosome / tRNA processing / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA intronic binding / protein-RNA complex assembly / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small 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
40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. ...40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / 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 / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / : / Ribosomal protein S17e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / : / 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 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / 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 S19e / Ribosomal protein S8e, conserved site / Ribosomal protein L27e superfamily / Ribosomal protein S19e / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS10B / Large ribosomal subunit protein eL8 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS10B / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS12A / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS7A / 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 / Small ribosomal subunit protein eS17A / Small ribosomal subunit protein uS4B / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30C / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL18B / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL24B / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL6B / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein eS1B / Large ribosomal subunit protein eL36B / Large ribosomal subunit protein eL37B / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein uS11B / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL14B / Small ribosomal subunit protein eS30B / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13B / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL2C / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS12A / Large ribosomal subunit protein uL5A / Small ribosomal subunit protein eS28A / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein uL3A / Large ribosomal subunit protein eL30A / Large ribosomal subunit protein uL15B / Small ribosomal subunit protein eS19A / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS25A / Large ribosomal subunit protein eL32A / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL16A / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL23A / Large ribosomal subunit protein eL18B / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein eS6B / Large ribosomal subunit protein eL43A / Small ribosomal subunit protein eS4C / Small ribosomal subunit protein eS8B / 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 / Small ribosomal subunit protein eS26B / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS19B / Small ribosomal subunit protein uS2A
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 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
AA: 18S ribosomal RNA
AD: Small ribosomal subunit protein uS2A
AE: Small ribosomal subunit protein eS1B
AF: Small ribosomal subunit protein uS5
AG: Small ribosomal subunit protein uS3
AH: Small ribosomal subunit protein eS4C
AI: Small ribosomal subunit protein uS7A
AJ: Small ribosomal subunit protein eS6B
AK: Small ribosomal subunit protein eS7
AL: Small ribosomal subunit protein eS8B
AM: Small ribosomal subunit protein uS4B
AN: Small ribosomal subunit protein eS10B
AO: Small ribosomal subunit protein uS17A
AP: Small ribosomal subunit protein eS12A
AQ: Small ribosomal subunit protein uS15
AR: Small ribosomal subunit protein uS11B
AS: Small ribosomal subunit protein uS19B
AT: Small ribosomal subunit protein uS9A
AU: Small ribosomal subunit protein eS17A
AV: Small ribosomal subunit protein uS13B
AW: Small ribosomal subunit protein eS19A
Aa: Small ribosomal subunit protein uS10
Ab: Small ribosomal subunit protein eS21
Ac: Small ribosomal subunit protein uS8A
Ad: Small ribosomal subunit protein uS12A
Ae: Small ribosomal subunit protein eS24A
Af: Small ribosomal subunit protein eS25A
Ag: Small ribosomal subunit protein eS26B
Ah: Small ribosomal subunit protein eS27
Ai: Small ribosomal subunit protein eS28A
Aj: Small ribosomal subunit protein uS14
Ak: Small ribosomal subunit protein eS30B
B0: Large ribosomal subunit protein eL42
B1: Large ribosomal subunit protein eL43A
B2: 28S ribosomal RNA
B3: 5S ribosomal RNA
B4: 5.8S ribosomal RNA
BN: Large ribosomal subunit protein uL2C
BO: Large ribosomal subunit protein uL3A
BP: Large ribosomal subunit protein uL4A
BQ: Large ribosomal subunit protein uL18B
BR: Large ribosomal subunit protein eL6
BS: Large ribosomal subunit protein uL30C
BT: Large ribosomal subunit protein eL8
BU: Large ribosomal subunit protein uL6B
BV: Large ribosomal subunit protein uL16A
BW: Large ribosomal subunit protein uL5A
BX: Large ribosomal subunit protein eL13
BY: Large ribosomal subunit protein eL14
BZ: Large ribosomal subunit protein eL15B
Ba: Large ribosomal subunit protein uL13A
Bb: Large ribosomal subunit protein uL22A
Bc: Large ribosomal subunit protein eL18B
Bd: Large ribosomal subunit protein eL19B
Be: Large ribosomal subunit protein eL20A
Bf: Large ribosomal subunit protein eL21B
Bg: Large ribosomal subunit protein eL22
Bh: Large ribosomal subunit protein uL14B
Bi: Large ribosomal subunit protein eL24B
Bj: Large ribosomal subunit protein uL23A
Bk: Large ribosomal subunit protein uL24
Bl: Large ribosomal subunit protein eL27A
Bm: Large ribosomal subunit protein uL15B
Bn: Large ribosomal subunit protein eL29
Bo: Large ribosomal subunit protein eL30A
Bp: Large ribosomal subunit protein eL31
Bq: Large ribosomal subunit protein eL32A
Br: Large ribosomal subunit protein eL33A
Bs: Large ribosomal subunit protein eL34B
Bt: Large ribosomal subunit protein uL29
Bu: Large ribosomal subunit protein eL36B
Bv: Large ribosomal subunit protein eL37B
Bw: Large ribosomal subunit protein eL38A
Bx: Large ribosomal subunit protein eL39
By: Large ribosomal subunit protein eL28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,150,25781
Polymers3,149,86575
Non-polymers3926
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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RNA chain , 4 types, 4 molecules AAB2B3B4

#1: RNA chain 18S ribosomal RNA


Mass: 593528.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: NR_151432.1
#35: 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
#36: 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
#37: 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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Small ribosomal subunit protein ... , 31 types, 31 molecules ADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAaAbAcAdAeAfAgAhAiAjAk

#2: Protein Small ribosomal subunit protein uS2A / 40S ribosomal protein S0-A


Mass: 31794.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9Y7L8
#3: Protein Small ribosomal subunit protein eS1B / 40S ribosomal protein S1-B / S3aE-B


Mass: 28574.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94438
#4: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 27681.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74892
#5: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 27594.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O60128
#6: Protein Small ribosomal subunit protein eS4C / 40S ribosomal protein S4-C


Mass: 29735.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P4W9
#7: Protein Small ribosomal subunit protein uS7A / 40S ribosomal protein S5-A


Mass: 22257.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14277
#8: Protein Small ribosomal subunit protein eS6B / 40S ribosomal protein S6-B


Mass: 27537.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9C0Z7
#9: Protein Small ribosomal subunit protein eS7 / 40S ribosomal protein S7


Mass: 21987.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10101
#10: Protein Small ribosomal subunit protein eS8B / 40S ribosomal protein S8-B


Mass: 22614.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7B2
#11: Protein Small ribosomal subunit protein uS4B / 40S ribosomal protein S9-B


Mass: 22290.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59675
#12: Protein Small ribosomal subunit protein eS10B / 40S ribosomal protein S10-B


Mass: 16470.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13614
#13: Protein Small ribosomal subunit protein uS17A / 40S ribosomal protein S11-A


Mass: 17535.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT73
#14: Protein Small ribosomal subunit protein eS12A / 40S ribosomal protein S12-A


Mass: 15632.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14062
#15: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 16985.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P28189
#16: Protein Small ribosomal subunit protein uS11B / 40S ribosomal protein S14-B


Mass: 14723.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT57
#17: Protein Small ribosomal subunit protein uS19B / 40S ribosomal protein S15-B


Mass: 17667.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTQ6
#18: Protein Small ribosomal subunit protein uS9A / 40S ribosomal protein S16-A


Mass: 15424.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT64
#19: Protein Small ribosomal subunit protein eS17A / 40S ribosomal protein S17-A


Mass: 15544.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42984
#20: Protein Small ribosomal subunit protein uS13B / 40S ribosomal protein S18-B


Mass: 17470.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT67
#21: Protein Small ribosomal subunit protein eS19A / 40S ribosomal protein S19-A / S16-A


Mass: 16178.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P58234
#22: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13569.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74893
#23: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21 / S28


Mass: 9627.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05764
#24: Protein Small ribosomal subunit protein uS8A / 40S ribosomal protein S22-A


Mass: 14785.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT58
#25: Protein Small ribosomal subunit protein uS12A / 40S ribosomal protein S23-A


Mass: 15691.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT75
#26: Protein Small ribosomal subunit protein eS24A / 40S ribosomal protein S24-A


Mass: 15506.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13784
#27: Protein Small ribosomal subunit protein eS25A / 40S ribosomal protein S25-A / S31-A


Mass: 9979.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79009
#28: Protein Small ribosomal subunit protein eS26B / 40S ribosomal protein S26-B


Mass: 13895.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTG4
#29: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27


Mass: 9185.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74330
#30: Protein Small ribosomal subunit protein eS28A / 40S ribosomal protein S28-A / S33


Mass: 7678.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT79
#31: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6672.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74329
#32: Protein Small ribosomal subunit protein eS30B / 40S ribosomal protein S30-B


Mass: 6928.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT63

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Large ribosomal subunit protein ... , 40 types, 40 molecules B0B1BNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBeBfBgBhBiBjBkBlBmBnBo...

#33: 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
#34: 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
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: 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
#48: 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
#49: 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
#50: 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
#51: 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
#52: 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
#53: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#65: 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
#66: 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
#67: 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
#68: 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
#69: 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
#70: 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
#71: 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
#72: 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
#73: 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
#74: 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
#75: 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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Non-polymers , 1 types, 6 molecules

#76: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

-
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 / Type: RIBOSOME / Entity ID: #1-#75 / 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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73376 / Algorithm: BACK PROJECTION / 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: 46.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034209364
ELECTRON MICROSCOPYf_angle_d0.5209307858
ELECTRON MICROSCOPYf_chiral_restr0.030438589
ELECTRON MICROSCOPYf_plane_restr0.003719838
ELECTRON MICROSCOPYf_dihedral_angle_d15.18974055

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