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- PDB-9cai: High-resolution C. elegans 80S ribosome structure - class 1 -

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Basic information

Entry
Database: PDB / ID: 9cai
TitleHigh-resolution C. elegans 80S ribosome structure - class 1
Components
  • (Large ribosomal subunit protein ...) x 37
  • (Small ribosomal subunit protein ...) x 28
  • (Ubiquitin-like ...) x 2
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S ribosomal protein L29
  • Plectin/S10 N-terminal domain-containing protein
  • Ribosomal Protein, Small subunit
  • Ribosomal protein L37
  • Ubiquitin-ribosomal protein eL40 fusion protein
  • eL41
  • mRNA
  • tRNA
KeywordsRIBOSOME / endogenous purified 80S ribosome
Function / homology
Function and homology information


Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / mTORC1-mediated signalling / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of PLK1 Activity at G2/M Transition ...Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / mTORC1-mediated signalling / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of PLK1 Activity at G2/M Transition / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / ABC-family proteins mediated transport / Degradation of DVL / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hedgehog ligand biogenesis / Hedgehog 'on' state / Translesion synthesis by POLK / Translesion synthesis by POLI / Negative regulation of MAPK pathway / MAPK6/MAPK4 signaling / UCH proteinases / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Major pathway of rRNA processing in the nucleolus and cytosol / CDK-mediated phosphorylation and removal of Cdc6 / Cyclin D associated events in G1 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / GTP hydrolysis and joining of the 60S ribosomal subunit / Ubiquitin-dependent degradation of Cyclin D / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Protein hydroxylation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Downregulation of ERBB4 signaling / Formation of Incision Complex in GG-NER / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / Aggrephagy / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / L13a-mediated translational silencing of Ceruloplasmin expression / Stimuli-sensing channels / Orc1 removal from chromatin / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Neddylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Metalloprotease DUBs / Downregulation of ERBB2 signaling / Negative regulators of DDX58/IFIH1 signaling / RAS processing / Degradation of beta-catenin by the destruction complex / Regulation of TNFR1 signaling / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Ovarian tumor domain proteases / Negative regulation of MET activity / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / Peroxisomal protein import / Regulation of signaling by CBL / Ub-specific processing proteases / Clathrin-mediated endocytosis / polarity specification of anterior/posterior axis / cytoplasmic side of rough endoplasmic reticulum membrane / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / rough endoplasmic reticulum / 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 / determination of adult lifespan / small-subunit processome / positive regulation of apoptotic signaling pathway / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis
Similarity search - Function
Ribosomal protein L30e / Ribosomal protein L23 / : / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. ...Ribosomal protein L30e / Ribosomal protein L23 / : / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / S27a-like superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein S7e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal_L40e / Ribosomal protein L40e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L40e superfamily / 40S ribosomal protein S4 C-terminus / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein S8e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S8e signature. / Ribosomal protein L30e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site
Similarity search - Domain/homology
Chem-3HE / SPERMIDINE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...Chem-3HE / SPERMIDINE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL24 / Plectin/S10 N-terminal domain-containing protein / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL19 / Ribosomal Protein, Small subunit / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL20 / 60S ribosomal protein L29 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL18 / Ribosomal protein L37 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Ubiquitin-like protein 1-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein uL18 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein uL16 / Ubiquitin-like domain-containing protein / Large ribosomal subunit protein uL5B / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL23B / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL30
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsSehgal, E. / Serrao, V.H.B. / Arribere, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM131012 United States
CitationJournal: RNA / Year: 2024
Title: High-resolution reconstruction of a ribosome sheds light on evolutionary dynamics and tissue specificity.
Authors: Enisha Sehgal / Chloe Wohlenberg / Evan M Soukup / Marcus J Viscardi / Vitor Hugo Balasco Serrão / Joshua A Arribere /
Abstract: is an important model organism for human health and disease, with foundational contributions to the understanding of gene expression and tissue patterning in animals. An invaluable tool in modern ... is an important model organism for human health and disease, with foundational contributions to the understanding of gene expression and tissue patterning in animals. An invaluable tool in modern gene expression research is the presence of a high-resolution ribosome structure, though no such structure exists for Here, we present a high-resolution single-particle cryogenic electron microscopy (cryo-EM) reconstruction and molecular model of a ribosome, revealing a significantly streamlined animal ribosome. Many facets of ribosome structure are conserved in , including overall ribosomal architecture and the mechanism of cycloheximide, whereas other facets, such as expansion segments and eL28, are rapidly evolving. We identify uL5 and uL23 as two instances of tissue-specific ribosomal protein paralog expression conserved in , suggesting that ribosomes vary across tissues. The ribosome structure will provide a basis for future structural, biochemical, and genetic studies of translation in this important animal system.
History
DepositionJun 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Data collection / Structure summary / Category: em_admin / struct
Item: _em_admin.last_update / _em_admin.title / _struct.title
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Small ribosomal subunit protein uS2
CA: Large ribosomal subunit protein uL2
DA: tRNA
AB: Small ribosomal subunit protein eS1
CB: Large ribosomal subunit protein uL3
AC: Small ribosomal subunit protein uS5
AD: Small ribosomal subunit protein uS3
AE: Small ribosomal subunit protein eS4
A7: 5S rRNA
A8: 5.8S rRNA
B2: 18S rRNA
A5: 28S rRNA
AR: Small ribosomal subunit protein eS17
AK: Plectin/S10 N-terminal domain-containing protein
AW: Ribosomal Protein, Small subunit
AS: Small ribosomal subunit protein uS13
AT: Small ribosomal subunit protein eS19
Aa: Small ribosomal subunit protein eS26
Af: Ubiquitin-like protein 1-ribosomal protein eS31 fusion protein
AO: Small ribosomal subunit protein uS11
AI: Small ribosomal subunit protein eS8
AF: Small ribosomal subunit protein uS7
AM: Small ribosomal subunit protein eS12
AV: Small ribosomal subunit protein eS21
AN: Small ribosomal subunit protein uS15
AZ: Small ribosomal subunit protein eS25
Ad: Small ribosomal subunit protein uS14
AY: Small ribosomal subunit protein eS24
AU: Small ribosomal subunit protein uS10
AG: Small ribosomal subunit protein eS6
Ab: Small ribosomal subunit protein eS27
AP: Small ribosomal subunit protein uS19
Ac: Small ribosomal subunit protein eS28
Ae: Ubiquitin-like domain-containing protein
AX: Small ribosomal subunit protein uS12
AL: Small ribosomal subunit protein uS17
AJ: Small ribosomal subunit protein uS4
AQ: Small ribosomal subunit protein uS9
AH: Small ribosomal subunit protein eS7
CF: Large ribosomal subunit protein uL30
CS: Large ribosomal subunit protein eL20
CV: Large ribosomal subunit protein uL14
CU: Large ribosomal subunit protein eL22
CL: Large ribosomal subunit protein eL13
CG: Large ribosomal subunit protein eL8
CI: Large ribosomal subunit protein uL16
CO: Large ribosomal subunit protein uL13
CC: Large ribosomal subunit protein uL4
Ch: Large ribosomal subunit protein uL29
CE: Large ribosomal subunit protein eL6
Co: Large ribosomal subunit protein eL42
Cf: Large ribosomal subunit protein eL33
Ci: Large ribosomal subunit protein eL36
Cl: Large ribosomal subunit protein eL39
CN: Large ribosomal subunit protein eL15
Ca: Large ribosomal subunit protein uL15
Cp: Large ribosomal subunit protein eL43
CM: Large ribosomal subunit protein eL14
Cc: Large ribosomal subunit protein eL30
CH: Large ribosomal subunit protein uL6
CY: Large ribosomal subunit protein uL24
CR: Large ribosomal subunit protein eL19
Cb: 60S ribosomal protein L29
CQ: Large ribosomal subunit protein eL18
CT: Large ribosomal subunit protein eL21
CD: Large ribosomal subunit protein uL18
CZ: Large ribosomal subunit protein eL27
CP: Large ribosomal subunit protein uL22
Cn: eL41
Cg: Large ribosomal subunit protein eL34
Ck: Large ribosomal subunit protein eL38
Cm: Ubiquitin-ribosomal protein eL40 fusion protein
Cd: Large ribosomal subunit protein eL31
Ce: Large ribosomal subunit protein eL32
CW: Large ribosomal subunit protein eL24
Cj: Ribosomal protein L37
CJ: Large ribosomal subunit protein uL5B
CX: Large ribosomal subunit protein uL23B
DC: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,163,65381
Polymers3,163,22779
Non-polymers4272
Water00
1


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

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Components

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Small ribosomal subunit protein ... , 28 types, 28 molecules AAABACADAEARASATAaAOAIAFAMAVANAZAdAYAUAGAbAPAcAXALAJAQAH

#1: Protein Small ribosomal subunit protein uS2 / 40S ribosomal protein SA


Mass: 30735.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P46769
#4: Protein Small ribosomal subunit protein eS1 / 40S ribosomal protein S3a


Mass: 29014.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P48154
#6: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 29011.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P51403
#7: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 27356.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P48152
#8: Protein Small ribosomal subunit protein eS4 / 40S ribosomal protein S4


Mass: 29101.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9N3X2
#13: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 14966.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O01692
#16: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17809.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O18240
#17: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 16355.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O18650
#18: Protein Small ribosomal subunit protein eS26 / 40S ribosomal protein S26


Mass: 13282.554 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O45499
#20: Protein Small ribosomal subunit protein uS11 / 40S ribosomal protein S14


Mass: 16278.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P48150
#21: Protein Small ribosomal subunit protein eS8 / 40S ribosomal protein S8


Mass: 23800.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P48156
#22: Protein Small ribosomal subunit protein uS7 / 40S ribosomal protein S5


Mass: 23189.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P49041
#23: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 15092.263 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P49196
#24: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9688.956 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P49197
#25: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17354.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P51404
#26: Protein Small ribosomal subunit protein eS25 / 40S ribosomal protein S25


Mass: 12943.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P52821
#27: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6568.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P90983
#28: Protein Small ribosomal subunit protein eS24 / 40S ribosomal protein S24


Mass: 14908.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q1XFY9
#29: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13258.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q8WQA8
#30: Protein Small ribosomal subunit protein eS6 / 40S ribosomal protein S6


Mass: 28201.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9NEN6
#31: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27


Mass: 9364.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9TXP0
#32: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15


Mass: 17279.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9XVP0
#33: Protein Small ribosomal subunit protein eS28 / 40S ribosomal protein S28


Mass: 7449.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q95Y04
#35: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15909.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q19877
#36: Protein Small ribosomal subunit protein uS17 / 40S ribosomal protein S11


Mass: 17782.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q20206
#37: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 22006.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q20228
#38: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16348.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q22054
#39: Protein Small ribosomal subunit protein eS7 / 40S ribosomal protein S7


Mass: 22100.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q23312

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Large ribosomal subunit protein ... , 37 types, 37 molecules CACBCFCSCVCUCLCGCICOCCChCECoCfCiClCNCaCpCMCcCHCYCRCQCTCDCZCP...

#2: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28267.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9XVF7
#5: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3


Mass: 45759.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P50880
#40: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 28185.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O01802
#41: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 21001.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O44480
#42: Protein Large ribosomal subunit protein uL14 / 60S ribosomal protein L23


Mass: 14979.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P48158
#43: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 14979.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P52819
#44: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13


Mass: 23809.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P91128
#45: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a


Mass: 30240.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q966C6
#46: Protein Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / QM protein homolog


Mass: 24800.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q09533
#47: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a


Mass: 23044.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q27389
#48: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4


Mass: 38735.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O02056
#49: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14232.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P34662
#50: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6


Mass: 24364.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P47991
#51: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L44 / L41 / Ribosomal protein rpl-36.A


Mass: 12403.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P48166
#52: Protein Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a


Mass: 13797.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P49180
#53: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 11916.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P49181
#54: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6347.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P52814
#55: Protein Large ribosomal subunit protein eL15 / 60S ribosomal protein L15


Mass: 24187.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P91374
#56: Protein Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a


Mass: 16245.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9BKU5
#57: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10126.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9U2A8
#58: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 15384.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9XVE9
#59: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12453.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9XWS4
#60: Protein Large ribosomal subunit protein uL6 / 60S ribosomal protein L9


Mass: 21545.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q95Y90
#61: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 16117.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q19869
#62: Protein Large ribosomal subunit protein eL19 / 60S ribosomal protein L19


Mass: 23715.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O02639
#64: Protein Large ribosomal subunit protein eL18 / 60S ribosomal protein L18


Mass: 21042.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O45946
#65: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18349.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P34334
#66: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 33451.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P49405
#67: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15765.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P91914
#68: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21560.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9BL19
#70: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 12712.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: A3QMC5
#71: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8096.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O17570
#73: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 14291.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9U332
#74: Protein Large ribosomal subunit protein eL32 / 60S ribosomal protein L32


Mass: 15554.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q22716
#75: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24


Mass: 17825.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O01868
#77: Protein Large ribosomal subunit protein uL5B / 60S ribosomal protein L11-2


Mass: 22823.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q19162
#78: Protein Large ribosomal subunit protein uL23B / 60S ribosomal protein L23a 2


Mass: 16320.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q20647

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RNA chain , 6 types, 6 molecules DAA7A8B2A5DC

#3: RNA chain tRNA


Mass: 24533.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: GenBank: 351064414
#9: RNA chain 5S rRNA


Mass: 38254.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: GenBank: 6842
#10: RNA chain 5.8S rRNA


Mass: 49250.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: GenBank: 6830
#11: RNA chain 18S rRNA


Mass: 565164.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: GenBank: 25167357
#12: RNA chain 28S rRNA


Mass: 1132082.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: GenBank: 2112362711
#79: RNA chain mRNA


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata)

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Protein , 5 types, 5 molecules AKAWCbCmCj

#14: Protein Plectin/S10 N-terminal domain-containing protein


Mass: 16897.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O01869
#15: Protein Ribosomal Protein, Small subunit


Mass: 14758.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O17218
#63: Protein 60S ribosomal protein L29


Mass: 7249.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O45226
#72: Protein Ubiquitin-ribosomal protein eL40 fusion protein / CEP52


Mass: 14680.231 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P49632
#76: Protein Ribosomal protein L37


Mass: 10536.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O62388

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Ubiquitin-like ... , 2 types, 2 molecules AfAe

#19: Protein Ubiquitin-like protein 1-ribosomal protein eS31 fusion protein


Mass: 18135.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P37165
#34: Protein Ubiquitin-like domain-containing protein


Mass: 14058.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q18231

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Protein/peptide , 1 types, 1 molecules Cn

#69: Protein/peptide eL41


Mass: 3012.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata)

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Non-polymers , 2 types, 2 molecules

#80: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#81: Chemical ChemComp-3HE / 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione


Mass: 281.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO4

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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: Caenorhabditis elegans 80S ribosome / Type: RIBOSOME / Entity ID: #1-#79 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40.94 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8337

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2SerialEMv4.93image acquisition
4cryoSPARC4.4.1CTF correction
7Cootmodel fitting
9PHENIX1.20.1_4487:model refinement
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.1classification
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 695837
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145659 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 59.4 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 92.48 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035202404
ELECTRON MICROSCOPYf_angle_d0.5564296495
ELECTRON MICROSCOPYf_chiral_restr0.040536975
ELECTRON MICROSCOPYf_plane_restr0.004519666
ELECTRON MICROSCOPYf_dihedral_angle_d15.655369992

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