6TB3

yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Ccr4-Not complex monitors the translating ribosome for codon optimality.

Buschauer, R.Matsuo, Y.Sugiyama, T.Chen, Y.H.Alhusaini, N.Sweet, T.Ikeuchi, K.Cheng, J.Matsuki, Y.Nobuta, R.Gilmozzi, A.Berninghausen, O.Tesina, P.Becker, T.Coller, J.Inada, T.Beckmann, R.

(2020) Science 368

  • DOI: https://doi.org/10.1126/science.aay6912
  • Primary Citation of Related Structures:  
    6TB3, 6TNU

  • PubMed Abstract: 

    Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.


  • Organizational Affiliation

    Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AC [auth P]206Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AD [auth Q]232Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15117Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2F [auth R]216Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3G [auth A]222Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AH [auth S]258Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5I [auth B]206Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AJ [auth T]228Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AK [auth U]184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8L [auth V]187Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for A0A0J9X221 (Lachancea kluyveri)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AM [auth W]184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AN [auth C]92Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AO [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12P [auth D]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13Q [auth Y]150Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BR [auth Z]127Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AS [auth F]141Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-BT [auth G]125Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AU [auth H]145Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AV [auth I]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20W [auth J]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AY [auth a]87Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AZ [auth b]129Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AAA [auth c]144Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-ABA [auth d]134Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-ACA [auth K]82Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-BDA [auth e]97Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AEA [auth f]81Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-AFA [auth M]53Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AGA [auth g]60Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31HA [auth N]73Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinIA [auth O]312Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AJA [auth L]63Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L1-ALA [auth BT]204Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AOA [auth AW]251Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3PA [auth BA]386Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AQA [auth BE]361Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5RA [auth BI]294Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-BSA [auth BM]175Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-ATA [auth BO]222Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AUA [auth AA]233Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AVA [auth AD]191Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10WA [auth BD]218Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BXA [auth AG]169Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AYA [auth AJ]193Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AZA [auth AM]136Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AAB [auth AQ]203Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-ABB [auth AU]197Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-ACB [auth AX]183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-ADB [auth BB]185Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AEB [auth BF]188Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AFB [auth BH]171Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AGB [auth BJ]159Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AHB [auth BL]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AIB [auth AB]136Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AJB [auth AE]126Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25KB [auth AH]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ALB [auth AK]125Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AMB [auth AN]135Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28NB [auth AR]148Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29OB [auth AV]58Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30PB [auth AY]96Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AQB [auth BC]109Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32RB [auth BG]127Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-ASB [auth BK]106Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-ATB [auth BN]112Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AUB [auth BP]119Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AVB [auth AC]99Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AWB [auth AF]81Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38XB [auth AI]77Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39YB [auth AL]50Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40ZB [auth AO]52Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-BAC [auth AS]25Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-ABC [auth AP]103Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-ACC [auth AT]91Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-ADC [auth BV]22Saccharomyces cerevisiae S288CMutation(s): 0 
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