7OLD

Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation.

Kisonaite, M., Wild, K., Lapouge, K., Ruppert, T., Sinning, I.

(2022) Nat Commun 13: 476-476

  • DOI: https://doi.org/10.1038/s41467-022-27967-9
  • Primary Citation of Related Structures:  
    7OLC, 7OLD

  • PubMed Abstract: 

    Ribosomes are complex and highly conserved ribonucleoprotein assemblies catalyzing protein biosynthesis in every organism. Here we present high-resolution cryo-EM structures of the 80S ribosome from a thermophilic fungus in two rotational states, which due to increased 80S stability provide a number of mechanistic details of eukaryotic translation. We identify a universally conserved 'nested base-triple knot' in the 26S rRNA at the polypeptide tunnel exit with a bulged-out nucleotide that likely serves as an adaptable element for nascent chain containment and handover. We visualize the structure and dynamics of the ribosome protective factor Stm1 upon ribosomal 40S head swiveling. We describe the structural impact of a unique and essential m 1 acp 3 Ψ 18S rRNA hyper-modification embracing the anticodon wobble-position for eukaryotic tRNA and mRNA translocation. We complete the eEF2-GTPase switch cycle describing the GDP-bound post-hydrolysis state. Taken together, our data and their integration into the structural landscape of 80S ribosomes furthers our understanding of protein biogenesis.

    • Organizational Affiliation: 

    Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany.


Macromolecules

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative guanine nucleotide-binding proteinF [auth A]316Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
HABP4_PAI-RBP1 domain-containing proteinG [auth B]302Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2H [auth C]845Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-like proteinI [auth LA]254Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3-like proteinJ [auth LB]392Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-like proteinK [auth LC]365Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l5-like proteinL [auth LD]304Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6M [auth LE]200Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l7-like proteinN [auth LF]249Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8O [auth LG]262Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l9-like proteinP [auth LH]229Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10-like proteinQ [auth LI]219Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal proteinR [auth LJ]173Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12-like proteinS [auth LK]165Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13T [auth LL]213Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-like proteinU [auth LM]142Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15V [auth LN]203Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-like proteinW [auth LO]204Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Find proteins for G0SH61 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l17-like proteinX [auth LP]187Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18-like proteinY [auth LQ]213Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19Z [auth LR]192Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20AA [auth LS]174Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l21-like proteinBA [auth LT]160Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-like proteinCA [auth LU]127Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l23-like proteinDA [auth LV]139Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-like proteinEA [auth LW]205Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25-like proteinFA [auth LX]156Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-like proteinGA [auth LY]138Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27HA [auth LZ]135Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28-like proteinIA [auth La]149Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JA [auth Lb]65Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l30-like proteinKA [auth Lc]108Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal proteinLA [auth Ld]120Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32-like proteinMA [auth Le]131Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l33-like proteinNA [auth Lf]109Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein l34-like proteinOA [auth Lg]119Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycotransferasePA [auth Lh]126Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 2.4.99.18
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36QA [auth Li]110Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37RA [auth Lj]95Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38-like proteinSA [auth Lk]94Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SG89 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL39TA [auth Ll]51Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinUA [auth Lm]127Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AVA [auth Ln],
ZA [auth Lr]		25Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L44-like proteinWA [auth Lo]106Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-like proteinXA [auth Lp]92Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal proteinYA [auth Lq]147Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0AB [auth Ls]312Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0BB [auth SA]285Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1CB [auth SB]255Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2-like proteinDB [auth SC]263Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3-like proteinEB [auth SD]254Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4FB [auth SE]264Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s5-like proteinGB [auth SF]212Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6HB [auth SG]239Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7IB [auth SH]203Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8JB [auth SI]202Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinKB [auth SJ]190Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s10-like proteinLB [auth SK]159Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinMB [auth SL]161Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12NB [auth SM]144Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13-like proteinOB [auth SN]151Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinPB [auth SO]150Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s15-like proteinQB [auth SP]153Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-like proteinRB [auth SQ]143Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-like proteinSB [auth SR]143Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal proteinTB [auth SS]156Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinUB [auth ST]153Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20-like proteinVB [auth SU]116Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-like proteinWB [auth SV]98Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-like proteinXB [auth SW]130Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s23-like proteinYB [auth SX]145Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24ZB [auth SY]136Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25AC [auth SZ]99Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26BC [auth Sa]119Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein s27-like proteinCC [auth Sb]82Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-like proteinDC [auth Sc]68Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS14EC [auth Sd]56Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30FC [auth Se]62Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27a-like proteinGC [auth Sf]154Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
26S rRNAA [auth 1]3,337Thermochaetoides thermophila DSM 1495
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S rRNAB [auth 2]1,796Thermochaetoides thermophila DSM 1495
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth 3]120Thermochaetoides thermophila DSM 1495
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S rRNAD [auth 4]156Thermochaetoides thermophila DSM 1495
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Entity ID: 5
MoleculeChains LengthOrganismImage
pe/E tRNAE [auth 5]75Thermochaetoides thermophila DSM 1495
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP
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JC [auth C]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN
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LC [auth Lg]
MC [auth Lj]
NC [auth Lm]
OC [auth Lo]
PC [auth Lp]
LC [auth Lg],
MC [auth Lj],
NC [auth Lm],
OC [auth Lo],
PC [auth Lp],
QC [auth Sa],
RC [auth Sb],
SC [auth Sd]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
HC [auth 1],
IC [auth 1],
KC [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DDE
Query on DDE		H [auth C]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references, Source and taxonomy