9CAI

High-resolution C. elegans 80S ribosome structure - class 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-Resolution Reconstruction of a C. elegans Ribosome Sheds Light on Evolutionary Dynamics and Tissue Specificity.

Sehgal, E.Wohlenberg, C.Soukup, E.M.Viscardi, M.J.Serrao, V.H.B.Arribere, J.A.

(2024) RNA 

  • DOI: https://doi.org/10.1261/rna.080103.124
  • Primary Citation of Related Structures:  
    9BH5, 9CAI

  • PubMed Abstract: 

    Caenorhabditis elegans 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 C. elegans. Here we present a high-resolution single-particle cryogenic electron microscopy (cryoEM) reconstruction and molecular model of a C. elegans ribosome, revealing a significantly streamlined animal ribosome. Many facets of ribosome structure are conserved in C. elegans, including overall ribosomal architecture and the mechanism of cycloheximide, while 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 Caenorhabditis, suggesting that C. elegans ribosomes vary across tissues. The C. elegans ribosome structure will provide a basis for future structural, biochemical, and genetic studies of translation in this important animal system.


  • Organizational Affiliation

    University of California at Santa Cruz; current address: Molecular Engineering and Sciences Institute at University of Washington.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2A [auth AA]276Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P46769 (Caenorhabditis elegans)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2B [auth CA]260Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9XVF7 (Caenorhabditis elegans)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1D [auth AB]257Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P48154 (Caenorhabditis elegans)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3E [auth CB]401Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P50880 (Caenorhabditis elegans)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5F [auth AC]272Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P51403 (Caenorhabditis elegans)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3G [auth AD]247Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4H [auth AE]259Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9N3X2 (Caenorhabditis elegans)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17M [auth AR]130Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O01692 (Caenorhabditis elegans)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Plectin/S10 N-terminal domain-containing proteinN [auth AK]149Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O01869 (Caenorhabditis elegans)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal Protein, Small subunitO [auth AW]130Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O17218 (Caenorhabditis elegans)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13P [auth AS]154Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O18240 (Caenorhabditis elegans)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19Q [auth AT]146Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O18650 (Caenorhabditis elegans)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS26R [auth Aa]117Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O45499 (Caenorhabditis elegans)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein 1-ribosomal protein eS31 fusion proteinS [auth Af]163Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P37165 (Caenorhabditis elegans)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11T [auth AO]152Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8U [auth AI]208Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7V [auth AF]210Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P49041 (Caenorhabditis elegans)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS12W [auth AM]140Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P49196 (Caenorhabditis elegans)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21X [auth AV]88Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15Y [auth AN]151Caenorhabditis elegansMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25Z [auth AZ]117Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P52821 (Caenorhabditis elegans)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14AA [auth Ad]56Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P90983 (Caenorhabditis elegans)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24BA [auth AY]131Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q1XFY9 (Caenorhabditis elegans)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10CA [auth AU]117Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q8WQA8 (Caenorhabditis elegans)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6DA [auth AG]246Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9NEN6 (Caenorhabditis elegans)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27EA [auth Ab]83Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9TXP0 (Caenorhabditis elegans)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19FA [auth AP]151Caenorhabditis elegansMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28GA [auth Ac]65Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like domain-containing proteinHA [auth Ae]130Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12IA [auth AX]143Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q19877 (Caenorhabditis elegans)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17JA [auth AL]155Caenorhabditis elegansMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4KA [auth AJ]189Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9LA [auth AQ]144Caenorhabditis elegansMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7MA [auth AH]194Caenorhabditis elegansMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30NA [auth CF]244Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20OA [auth CS]180Caenorhabditis elegansMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14PA [auth CV]140Caenorhabditis elegansMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22QA [auth CU]130Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13RA [auth CL]207Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8SA [auth CG]265Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16TA [auth CI]214Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13UA [auth CO]202Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4VA [auth CC]345Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29WA [auth Ch]123Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6XA [auth CE]217Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42YA [auth Co]105Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33ZA [auth Cf]124Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P49180 (Caenorhabditis elegans)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36AB [auth Ci]104Caenorhabditis elegansMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39BB [auth Cl]51Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL15CB [auth CN]204Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15DB [auth Ca]145Caenorhabditis elegansMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43EB [auth Cp]91Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14FB [auth CM]135Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30GB [auth Cc]115Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6HB [auth CH]189Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24IB [auth CY]142Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19JB [auth CR]198Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29KB [auth Cb]62Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O45226 (Caenorhabditis elegans)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18LB [auth CQ]188Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O45946 (Caenorhabditis elegans)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21MB [auth CT]161Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18NB [auth CD]293Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P49405 (Caenorhabditis elegans)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27OB [auth CZ]136Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P91914 (Caenorhabditis elegans)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22PB [auth CP]187Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
eL41QB [auth Cn]22Caenorhabditis elegansMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34RB [auth Cg]110Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38SB [auth Ck]70Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O17570 (Caenorhabditis elegans)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eL40 fusion proteinTB [auth Cm]128Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P49632 (Caenorhabditis elegans)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31UB [auth Cd]122Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9U332 (Caenorhabditis elegans)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32VB [auth Ce]134Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q22716 (Caenorhabditis elegans)
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24WB [auth CW]159Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O01868 (Caenorhabditis elegans)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37XB [auth Cj]92Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O62388 (Caenorhabditis elegans)
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5BYB [auth CJ]196Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q19162 (Caenorhabditis elegans)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23BZB [auth CX]146Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains LengthOrganismImage
tRNAC [auth DA]76Caenorhabditis elegans
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S rRNAI [auth A7]119Caenorhabditis elegans
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Entity ID: 10
MoleculeChains LengthOrganismImage
5.8S rRNAJ [auth A8]153Caenorhabditis elegans
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Entity ID: 11
MoleculeChains LengthOrganismImage
18S rRNAK [auth B2]1,754Caenorhabditis elegans
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Entity ID: 12
MoleculeChains LengthOrganismImage
28S rRNAL [auth A5]3,510Caenorhabditis elegans
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Entity ID: 79
MoleculeChains LengthOrganismImage
mRNAAC [auth DC]10Caenorhabditis elegans
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3HE
Query on 3HE

Download Ideal Coordinates CCD File 
CC [auth A5]4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
C15 H23 N O4
YPHMISFOHDHNIV-FSZOTQKASA-N
SPD
Query on SPD

Download Ideal Coordinates CCD File 
BC [auth A5]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM131012

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Data collection, Structure summary