9BDP

80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural mechanism of angiogenin activation by the ribosome.

Loveland, A.B.Koh, C.S.Ganesan, R.Jacobson, A.Korostelev, A.A.

(2024) Nature 630: 769-776

  • DOI: https://doi.org/10.1038/s41586-024-07508-8
  • Primary Citation of Related Structures:  
    9BDL, 9BDN, 9BDP

  • PubMed Abstract: 

    Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance 1-10 . After activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, resulting in translation repression 11-15 . However, the catalytic activity of isolated angiogenin is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle 3,16-23 . Here we identify these mechanisms using biochemical assays and cryogenic electron microscopy (cryo-EM). Our study reveals that the cytosolic ribosome is the activator of angiogenin. A cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic centre, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S-angiogenin structures capture how tRNA substrate is directed by the ribosome into angiogenin's active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, the abundance of which increases during cellular stress 24-27 . These results may facilitate the development of therapeutics to treat cancer and neurodegenerative diseases.


  • Organizational Affiliation

    RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA. anna.loveland@umassmed.edu.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth AL02]248Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3F [auth AL03]394Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4G [auth AL04]362Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9DCT1 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5H [auth AL05]293Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth AL06]251Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7J [auth AL07]225Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8K [auth AL08]240Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9L [auth AL09]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10M [auth AL10]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11N [auth AL11]170Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL11O [auth AL12]153Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13P [auth AL13]210Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TKB3 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14Q [auth AL14]138Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15R [auth AL15]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13S [auth AL16]199Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TVS8 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17T [auth AL17]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18U [auth AL18]187Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TFE0 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19V [auth AL19]180Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TYL6 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aW [auth AL20]176Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTY7 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21X [auth AL21]159Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22Y [auth AL22]99Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23Z [auth AL23]131Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24AA [auth AL24]121Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23BA [auth AL25]118Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26CA [auth AL26]134Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27DA [auth AL27]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aEA [auth AL28]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29FA [auth AL29]245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30GA [auth AL30]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31HA [auth AL31]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32IA [auth AL32]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aJA [auth AL33]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34KA [auth AL34]114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35LA [auth AL35]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36MA [auth AL36]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37NA [auth AL37]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38OA [auth AL38]69Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39PA [auth AL39]50Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40QA [auth AL40]52Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P0DXC2 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL41RA [auth AL41]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eL42SA [auth AL42]104Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9D391 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aTA [auth AL43]91Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28UA [auth ALNW]124Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0VA [auth ALP0]196Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
AngiogeninWA [auth ANG]147Homo sapiensMutation(s): 0 
Gene Names: ANGRNASE5
EC: 3.1.27
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PHAROS:  P03950
GTEx:  ENSG00000214274 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1XA [auth ARAC]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S_SA_C domain-containing proteinYA [auth AS00]217Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aZA [auth AS01]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2AB [auth AS02]221Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3BB [auth AS03]228Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4CB [auth AS04]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5DB [auth AS05]191Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6EB [auth AS06]237Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7FB [auth AS07]189Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8GB [auth AS08]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9HB [auth AS09]185Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10IB [auth AS10]96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11JB [auth AS11]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12KB [auth AS12]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13LB [auth AS13]149Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11MB [auth AS14]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15NB [auth AS15]120Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9OB [auth AS16]142Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17PB [auth AS17]132Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18QB [auth AS18]144Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19RB [auth AS19]141Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20SB [auth AS20]100Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
eS21TB [auth AS21]83Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aUB [auth AS22]129Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23VB [auth AS23]141Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24WB [auth AS24]124Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25XB [auth AS25]254Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
eS26YB [auth AS26]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27ZB [auth AS27]83Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28AC [auth AS28]62Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29BC [auth AS29]55Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30CC [auth AS30]55Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 1-alphaDC [auth EF1A]458Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth A18S]1,869Oryctolagus cuniculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
28S rRNAB [auth A28S]3,601Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S rRNAC [auth A58S]156Oryctolagus cuniculus
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAD [auth A5S]120Oryctolagus cuniculus
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Entity ID: 83
MoleculeChains LengthOrganismImage
tRNAfMetEC [auth ETRN],
GC [auth PTRN]
77Escherichia coli
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Entity ID: 84
MoleculeChains LengthOrganismImage
mRNAFC [auth MRNA]28Homo sapiens
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Entity ID: 85
MoleculeChains LengthOrganismImage
tRNAAlaHC [auth TIRN]76Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN

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 StatesR01 GM127094

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release