7OLD image
Entry Detail
PDB ID:
7OLD
EMDB ID:
Keywords:
Title:
Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state
Biological Source:
PDB Version:
Deposition Date:
2021-05-19
Release Date:
2022-01-26
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:26S rRNA
Chain IDs:A (auth: 1)
Chain Length:3337
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:B (auth: 2)
Chain Length:1796
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:C (auth: 3)
Chain Length:120
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:D (auth: 4)
Chain Length:156
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polyribonucleotide
Description:pe/E tRNA
Chain IDs:E (auth: 5)
Chain Length:75
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Putative guanine nucleotide-binding protein
Chain IDs:F (auth: A)
Chain Length:316
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:HABP4_PAI-RBP1 domain-containing protein
Chain IDs:G (auth: B)
Chain Length:302
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Elongation factor 2
Chain IDs:H (auth: C)
Chain Length:845
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L2-like protein
Chain IDs:I (auth: LA)
Chain Length:254
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3-like protein
Chain IDs:J (auth: LB)
Chain Length:65
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4-like protein
Chain IDs:K (auth: LC)
Chain Length:365
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein l5-like protein
Chain IDs:L (auth: LD)
Chain Length:304
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:M (auth: LE)
Chain Length:200
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein l7-like protein
Chain IDs:N (auth: LF)
Chain Length:249
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8
Chain IDs:O (auth: LG)
Chain Length:119
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein l9-like protein
Chain IDs:P (auth: LH)
Chain Length:229
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10-like protein
Chain IDs:Q (auth: LI)
Chain Length:110
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Putative ribosomal protein
Chain IDs:R (auth: LJ)
Chain Length:95
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L12-like protein
Chain IDs:S (auth: LK)
Chain Length:94
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13
Chain IDs:T (auth: LL)
Chain Length:51
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14-like protein
Chain IDs:U (auth: LM)
Chain Length:142
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ribosomal protein L15
Chain IDs:V (auth: LN)
Chain Length:203
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L16-like protein
Chain IDs:W (auth: LO)
Chain Length:204
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein l17-like protein
Chain IDs:X (auth: LP)
Chain Length:92
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ribosomal protein L18-like protein
Chain IDs:Y (auth: LQ)
Chain Length:147
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ribosomal protein L19
Chain IDs:Z (auth: LR)
Chain Length:192
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L20
Chain IDs:AA (auth: LS)
Chain Length:312
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein l21-like protein
Chain IDs:BA (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22-like protein
Chain IDs:CA (auth: LU)
Chain Length:127
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein l23-like protein
Chain IDs:DA (auth: LV)
Chain Length:139
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24-like protein
Chain IDs:EA (auth: LW)
Chain Length:205
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L25-like protein
Chain IDs:FA (auth: LX)
Chain Length:156
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26-like protein
Chain IDs:GA (auth: LY)
Chain Length:138
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:HA (auth: LZ)
Chain Length:135
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28-like protein
Chain IDs:IA (auth: La)
Chain Length:254
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:JA (auth: Lb)
Chain Length:65
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein l30-like protein
Chain IDs:KA (auth: Lc)
Chain Length:365
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Putative 60S ribosomal protein
Chain IDs:LA (auth: Ld)
Chain Length:304
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32-like protein
Chain IDs:MA (auth: Le)
Chain Length:200
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein l33-like protein
Chain IDs:NA (auth: Lf)
Chain Length:249
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ribosomal protein l34-like protein
Chain IDs:OA (auth: Lg)
Chain Length:119
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Dolichyl-diphosphooligosaccharide--protein glycotransferase
Chain IDs:PA (auth: Lh)
Chain Length:229
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:QA (auth: Li)
Chain Length:110
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ribosomal protein L37
Chain IDs:RA (auth: Lj)
Chain Length:95
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38-like protein
Chain IDs:SA (auth: Lk)
Chain Length:94
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL39
Chain IDs:TA (auth: Ll)
Chain Length:51
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ubiquitin
Chain IDs:UA (auth: Lm)
Chain Length:142
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41-A
Chain IDs:VA (auth: Ln), ZA (auth: Lr)
Chain Length:203
Number of Molecules:2
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L44-like protein
Chain IDs:WA (auth: Lo)
Chain Length:204
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L43-like protein
Chain IDs:XA (auth: Lp)
Chain Length:92
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Putative 60S ribosomal protein
Chain IDs:YA (auth: Lq)
Chain Length:147
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:60S acidic ribosomal protein P0
Chain IDs:AB (auth: Ls)
Chain Length:312
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S0
Chain IDs:BB (auth: SA)
Chain Length:285
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S1
Chain IDs:CB (auth: SB)
Chain Length:255
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2-like protein
Chain IDs:DB (auth: SC)
Chain Length:263
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3-like protein
Chain IDs:EB (auth: SD)
Chain Length:254
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4
Chain IDs:FB (auth: SE)
Chain Length:62
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein s5-like protein
Chain IDs:GB (auth: SF)
Chain Length:212
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6
Chain IDs:HB (auth: SG)
Chain Length:239
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:IB (auth: SH)
Chain Length:203
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:JB (auth: SI)
Chain Length:202
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein s9-like protein
Chain IDs:KB (auth: SJ)
Chain Length:190
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein s10-like protein
Chain IDs:LB (auth: SK)
Chain Length:159
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11-like protein
Chain IDs:MB (auth: SL)
Chain Length:161
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S12
Chain IDs:NB (auth: SM)
Chain Length:144
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S13-like protein
Chain IDs:OB (auth: SN)
Chain Length:151
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S14-like protein
Chain IDs:PB (auth: SO)
Chain Length:150
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein s15-like protein
Chain IDs:QB (auth: SP)
Chain Length:153
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S16-like protein
Chain IDs:RB (auth: SQ)
Chain Length:143
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17-like protein
Chain IDs:SB (auth: SR)
Chain Length:143
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Putative ribosomal protein
Chain IDs:TB (auth: SS)
Chain Length:156
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19-like protein
Chain IDs:UB (auth: ST)
Chain Length:153
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S20-like protein
Chain IDs:VB (auth: SU)
Chain Length:116
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21-like protein
Chain IDs:WB (auth: SV)
Chain Length:98
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S22-like protein
Chain IDs:XB (auth: SW)
Chain Length:130
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein s23-like protein
Chain IDs:YB (auth: SX)
Chain Length:145
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:ZB (auth: SY)
Chain Length:136
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:AC (auth: SZ)
Chain Length:99
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26
Chain IDs:BC (auth: Sa)
Chain Length:285
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ribosomal protein s27-like protein
Chain IDs:CC (auth: Sb)
Chain Length:255
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28-like protein
Chain IDs:DC (auth: Sc)
Chain Length:263
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:Ribosomal protein uS14
Chain IDs:EC (auth: Sd)
Chain Length:254
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30
Chain IDs:FC (auth: Se)
Chain Length:62
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27a-like protein
Chain IDs:GC (auth: Sf)
Chain Length:212
Number of Molecules:1
Biological Source:Chaetomium thermophilum var. thermophilum DSM 1495
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
DDE H HIS modified residue
Primary Citation
High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation.
Nat Commun 13 476 476 (2022)
PMID: 35079002 DOI: 10.1038/s41467-022-27967-9

Abstact

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 m1acp3 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.

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Primary Citation of related structures