8K2D

Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 basis for differential inhibition of eukaryotic ribosomes by tigecycline.

Li, X., Wang, M., Denk, T., Buschauer, R., Li, Y., Beckmann, R., Cheng, J.

(2024) Nat Commun 15: 5481-5481

  • DOI: https://doi.org/10.1038/s41467-024-49797-7
  • Primary Citation of Related Structures:  
    8K2A, 8K2B, 8K2C, 8K2D, 8K82, 8XSX, 8XSY, 8XSZ, 8XT0, 8XT1, 8XT2, 8XT3, 8YOO, 8YOP

  • PubMed Abstract: 

    Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, even though it is also cytotoxic for human cells, the molecular mechanism of its inhibition remains unclear. Here, we present cryo-EM structures of tigecycline-bound human mitochondrial 55S, 39S, cytoplasmic 80S and yeast cytoplasmic 80S ribosomes. We find that at clinically relevant concentrations, tigecycline effectively targets human 55S mitoribosomes, potentially, by hindering A-site tRNA accommodation and by blocking the peptidyl transfer center. In contrast, tigecycline does not bind to human 80S ribosomes under physiological concentrations. However, at high tigecycline concentrations, in addition to blocking the A-site, both human and yeast 80S ribosomes bind tigecycline at another conserved binding site restricting the movement of the L1 stalk. In conclusion, the observed distinct binding properties of tigecycline may guide new pathways for drug design and therapy.

    • Organizational Affiliation: 

    Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2AE [auth SA]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AF [auth SB]255Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2G [auth SC]254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3H [auth SD]240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AI [auth SE]261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7J [auth SF]225Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AK [auth SG]236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AL [auth SH]190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AM [auth SI]200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AN [auth SJ]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS10AO [auth SK]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17AP [auth SL]156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS12Q [auth SM]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13R [auth SN]151Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AS [auth SO]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19T [auth SP]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9AU [auth SQ]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17AV [auth SR]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13AW [auth SS]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19AX [auth ST]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10Y [auth SU]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21AZ [auth SV]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AAA [auth SW]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ABA [auth SX]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-ACA [auth SY]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25ADA [auth SZ]108Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS26BEA [auth Sa]119Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AFA [auth Sb]82Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28AGA [auth Sc]67Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14AHA [auth Sd]56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AIA [auth Se]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eS31 fusion proteinJA [auth Sf]152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1KA [auth Sg]319Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2A254Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3MA [auth LB]387Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4ANA [auth LC]362Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18OA [auth LD]297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6APA [auth LE]176Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30AQA [auth LF]244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8ARA [auth LG]256Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6ASA [auth LH]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16TA [auth LI]221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5AUA [auth LJ]174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL11AVA [auth LK]165Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13AWA [auth LL]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14AXA [auth LM]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL15AYA [auth LN]204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13AZA [auth LO]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22AAB [auth LP]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18ABB [auth LQ]186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19ACB [auth LR]189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20ADB [auth LS]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21AEB [auth LT]160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22AFB [auth LU]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14AGB [auth LV]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24AHB [auth LW]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23IB [auth LX]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24AJB [auth LY]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27AKB [auth LZ]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15LB [auth La]149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29MB [auth Lb]59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30NB [auth Lc]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31AOB [auth Ld]113Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32PB [auth Le]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33AQB [auth Lf]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34ARB [auth Lg]121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29ASB [auth Lh]120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36ATB [auth Li]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37AUB [auth Lj]88Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38VB [auth Lk]78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39WB [auth Ll]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eL40A fusion proteinXB [auth Lm]128Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL41AYB [auth Ln]25Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42AZB [auth Lo]106Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43AAC [auth Lp]92Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5A-1BC [auth CE]157Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1ACC [auth L1]217Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10DC [auth P0]312Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2EC [auth CD]842Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.5
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor protein STM1FC [auth CS]273Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth C2]1,800Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S rRNAB [auth C1]3,396Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth C4]121Saccharomyces cerevisiae
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S rRNAD [auth C3]158Saccharomyces cerevisiae
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T1C
Query on T1C
Download Ideal Coordinates CCD File 
HC [auth C1]
IC [auth C1]
JC [auth C1]
KC [auth C1]
LC [auth C1]
HC [auth C1],
IC [auth C1],
JC [auth C1],
KC [auth C1],
LC [auth C1],
MC [auth C1]
TIGECYCLINE
C29 H41 N5 O8
FPZLLRFZJZRHSY-HJYUBDRYSA-P
GDP
Query on GDP
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ZC [auth CD]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN
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GC [auth C2]
QC [auth SM]
RC [auth Sa]
SC [auth Sb]
TC [auth Lg]
GC [auth C2],
QC [auth SM],
RC [auth Sa],
SC [auth Sb],
TC [auth Lg],
UC [auth Lj],
VC [auth Lm],
WC [auth Lo],
XC [auth Lp]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
NC [auth C1],
OC [auth C1],
PC [auth C3],
YC [auth CD]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
5CT
Query on 5CT		BC [auth CE]PEPTIDE LINKINGC10 H23 N3 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release