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- PDB-7olc: Thermophilic eukaryotic 80S ribosome at idle POST state -

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Basic information

Entry
Database: PDB / ID: 7olc
TitleThermophilic eukaryotic 80S ribosome at idle POST state
Components
  • (40S ribosomal protein ...) x 29
  • (60S ribosomal protein ...) x 32
  • (Putative 60S ribosomal ...) x 2
  • (Putative ribosomal ...) x 2
  • (Ribosomal protein ...) x 6
  • 18S rRNA
  • 26S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • Dolichyl-diphosphooligosaccharide--protein glycotransferase
  • HABP4_PAI-RBP1 domain-containing protein
  • Putative guanine nucleotide-binding protein
  • Ribosome-associated molecular chaperone SSB1
  • Ubiquitin
  • eL39
  • uS14
KeywordsRIBOSOME / thermophilic eukaryotic ribosome / 80S / rRNA modifications / nascent chain
Function / homology
Function and homology information


RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / nucleolar large rRNA transcription by RNA polymerase I / non-chaperonin molecular chaperone ATPase / 90S preribosome / protein-RNA complex assembly ...RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / nucleolar large rRNA transcription by RNA polymerase I / non-chaperonin molecular chaperone ATPase / 90S preribosome / protein-RNA complex assembly / translation regulator activity / endomembrane system / post-translational protein modification / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / ATP-dependent protein folding chaperone / rRNA processing / regulation of translation / ribosome biogenesis / large ribosomal subunit / ribosome binding / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / methylation / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / mRNA binding / nucleolus / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / nucleus / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / : / : / Hyaluronan / mRNA binding family / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / Rrn7/TAF1B, N-terminal cyclin domain / Rrn7/TAF1B, C-terminal cyclin domain ...Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / : / : / Hyaluronan / mRNA binding family / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / Rrn7/TAF1B, N-terminal cyclin domain / Rrn7/TAF1B, C-terminal cyclin domain / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Centrosomal protein CEP104-like, TOG domain / RNA binding protein HABP4/SERBP1 / : / STT3/PglB/AglB core domain / Stm1-like, N-terminal / Stm1 / Parkin co-regulated protein / Parkin co-regulated protein / TOG domain / TOG / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / HEAT-like repeat / HEAT repeat profile. / HEAT, type 2 / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / : / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Ribosomal protein L30e / Ribosomal protein L28e / 50S ribosomal protein L10, insertion domain superfamily / : / Ribosomal L28e/Mak16 / 60S ribosomal protein L10P, insertion domain / Ribosomal L28e protein family / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L10e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L19/L19e conserved site / : / Ribosomal protein L19e signature. / Ribosomal protein S7e signature. / Ribosomal protein S25 / S25 ribosomal protein
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L3-like protein / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / 60S ribosomal protein L26-like protein ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L3-like protein / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / 60S ribosomal protein L26-like protein / Ribosomal protein L15 / 40S ribosomal protein s10-like protein / 60S ribosomal protein L27 / 40S ribosomal protein S13-like protein / 40S ribosomal protein s15-like protein / 60S ribosomal protein L6 / dolichyl-diphosphooligosaccharide--protein glycotransferase / 60S ribosomal protein l9-like protein / 60S ribosomal protein l21-like protein / 40S ribosomal protein s9-like protein / Ribosomal protein L37 / 40S ribosomal protein S4 / 60S ribosomal protein L24-like protein / 60S ribosomal protein L14-like protein / Ribosomal protein s27-like protein / 40S ribosomal protein S25 / 40S ribosomal protein s5-like protein / 40S ribosomal protein S26 / 40S ribosomal protein S27a-like protein / 40S ribosomal protein S20-like protein / Hyaluronan/mRNA-binding protein domain-containing protein / 60S ribosomal protein L2-like protein / 60S ribosomal protein L25-like protein / 60S ribosomal protein L43-like protein / 40S ribosomal protein S3 / Putative ribosomal protein / 60S ribosomal protein L32-like protein / Small ribosomal subunit protein eS1 / 40S ribosomal protein S17-like protein / 40S ribosomal protein S7 / Putative ribosomal protein / 60S ribosomal protein L13 / Ribosomal protein L18-like protein / 40S ribosomal protein S28-like protein / Ribosomal protein L19 / Putative guanine nucleotide-binding protein / 60S ribosomal protein L8 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L36 / 40S ribosomal protein S16-like protein / 60S ribosomal protein L44-like protein / 60S ribosomal protein L20 / 60S ribosomal protein l33-like protein / Ribosome-associated molecular chaperone SSB1 / Putative 60S ribosomal protein / 60S ribosomal protein L22-like protein / Large ribosomal subunit protein uL18 / 60S ribosomal protein l30-like protein / 60S ribosomal protein L10-like protein / 40S ribosomal protein S11-like protein / 60S ribosomal protein L4-like protein / 40S ribosomal protein S19-like protein / 60S ribosomal protein l7-like protein / 40S ribosomal protein S14-like protein / Ribosomal protein l34-like protein / 60S ribosomal protein L38-like protein / 60S ribosomal protein L12-like protein / 60S acidic ribosomal protein P0 / 60S ribosomal protein L28-like protein / 60S ribosomal protein l17-like protein / 60S ribosomal protein L16-like protein / 40S ribosomal protein S12 / 40S ribosomal protein S22-like protein / Putative 60S ribosomal protein / Large ribosomal subunit protein uL5 / 40S ribosomal protein S21-like protein / 60S ribosomal protein l23-like protein / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS32A / 40S ribosomal protein S30 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L29 / 40S ribosomal protein S29
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKisonaite, M. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2022
Title: High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation.
Authors: Miglė Kišonaitė / Klemens Wild / Karine Lapouge / Thomas Ruppert / Irmgard Sinning /
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 ...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 macp 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.
History
DepositionMay 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 6, 2022Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method

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Structure visualization

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Assembly

Deposited unit
1: 26S rRNA
2: 18S rRNA
3: 5S rRNA
4: 5.8S rRNA
A: Putative guanine nucleotide-binding protein
B: HABP4_PAI-RBP1 domain-containing protein
C: Ribosome-associated molecular chaperone SSB1
LA: 60S ribosomal protein L2-like protein
LB: 60S ribosomal protein L3-like protein
LC: 60S ribosomal protein L4-like protein
LD: 60S ribosomal protein l5-like protein
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein l7-like protein
LG: 60S ribosomal protein L8
LH: 60S ribosomal protein l9-like protein
LI: 60S ribosomal protein L10-like protein
LJ: Putative ribosomal protein
LK: 60S ribosomal protein L12-like protein
LL: 60S ribosomal protein L13
LM: 60S ribosomal protein L14-like protein
LN: Ribosomal protein L15
LO: 60S ribosomal protein L16-like protein
LP: 60S ribosomal protein l17-like protein
LQ: Ribosomal protein L18-like protein
LR: Ribosomal protein L19
LS: 60S ribosomal protein L20
LT: 60S ribosomal protein l21-like protein
LU: 60S ribosomal protein L22-like protein
LV: 60S ribosomal protein l23-like protein
LW: 60S ribosomal protein L24-like protein
LX: 60S ribosomal protein L25-like protein
LY: 60S ribosomal protein L26-like protein
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L28-like protein
Lb: 60S ribosomal protein L29
Lc: 60S ribosomal protein l30-like protein
Ld: Putative 60S ribosomal protein
Le: 60S ribosomal protein L32-like protein
Lf: 60S ribosomal protein l33-like protein
Lg: Ribosomal protein l34-like protein
Lh: Dolichyl-diphosphooligosaccharide--protein glycotransferase
Li: 60S ribosomal protein L36
Lj: Ribosomal protein L37
Lk: 60S ribosomal protein L38-like protein
Ll: eL39
Lm: Ubiquitin
Ln: 60S ribosomal protein L41-A
Lo: 60S ribosomal protein L44-like protein
Lp: 60S ribosomal protein L43-like protein
Lq: Putative 60S ribosomal protein
Lr: 60S ribosomal protein L41-A
Ls: 60S acidic ribosomal protein P0
SA: 40S ribosomal protein S0
SB: 40S ribosomal protein S1
SC: 40S ribosomal protein S2-like protein
SD: 40S ribosomal protein S3-like protein
SE: 40S ribosomal protein S4
SF: 40S ribosomal protein s5-like protein
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: 40S ribosomal protein s9-like protein
SK: 40S ribosomal protein s10-like protein
SL: 40S ribosomal protein S11-like protein
SM: 40S ribosomal protein S12
SN: 40S ribosomal protein S13-like protein
SO: 40S ribosomal protein S14-like protein
SP: 40S ribosomal protein s15-like protein
SQ: 40S ribosomal protein S16-like protein
SR: 40S ribosomal protein S17-like protein
SS: Putative ribosomal protein
ST: 40S ribosomal protein S19-like protein
SU: 40S ribosomal protein S20-like protein
SV: 40S ribosomal protein S21-like protein
SW: 40S ribosomal protein S22-like protein
SX: 40S ribosomal protein s23-like protein
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sa: 40S ribosomal protein S26
Sb: Ribosomal protein s27-like protein
Sc: 40S ribosomal protein S28-like protein
Sd: uS14
Se: 40S ribosomal protein S30
Sf: 40S ribosomal protein S27a-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,315,118663
Polymers3,300,71684
Non-polymers14,401579
Water17,024945
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 4 molecules 1234

#1: RNA chain 26S rRNA


Mass: 1078730.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
#2: RNA chain 18S rRNA


Mass: 578887.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
#3: RNA chain 5S rRNA


Mass: 38596.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
#4: RNA chain 5.8S rRNA


Mass: 50147.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

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Protein , 8 types, 8 molecules ABCLhLlLmLsSd

#5: Protein Putative guanine nucleotide-binding protein


Mass: 35149.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S9U0
#6: Protein HABP4_PAI-RBP1 domain-containing protein


Mass: 32667.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S428
#7: Protein Ribosome-associated molecular chaperone SSB1 / Heat shock protein SSB1 / Hsp70 chaperone Ssb


Mass: 67110.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SCU5, non-chaperonin molecular chaperone ATPase
#41: Protein Dolichyl-diphosphooligosaccharide--protein glycotransferase


Mass: 14643.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase
#45: Protein eL39


Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: Q2H9R2
#46: Protein Ubiquitin


Mass: 14609.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S8G4
#51: Protein 60S acidic ribosomal protein P0


Mass: 33853.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SGP3
#81: Protein uS14


Mass: 6504.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: Q2HB68

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60S ribosomal protein ... , 32 types, 33 molecules LALBLCLDLELFLGLHLILKLLLMLOLPLSLTLULVLWLXLYLZLaLbLcLeLfLiLkLn...

#8: Protein 60S ribosomal protein L2-like protein


Mass: 27598.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S4P8
#9: Protein 60S ribosomal protein L3-like protein


Mass: 44456.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RXW1
#10: Protein 60S ribosomal protein L4-like protein


Mass: 39439.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SFC3
#11: Protein 60S ribosomal protein l5-like protein


Mass: 35034.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SEG2
#12: Protein 60S ribosomal protein L6


Mass: 22132.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S0D6
#13: Protein 60S ribosomal protein l7-like protein


Mass: 28821.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SFL0
#14: Protein 60S ribosomal protein L8


Mass: 29744.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SAJ9
#15: Protein 60S ribosomal protein l9-like protein


Mass: 21582.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S0E5
#16: Protein 60S ribosomal protein L10-like protein


Mass: 25255.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SEI1
#18: Protein 60S ribosomal protein L12-like protein


Mass: 17802.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SGH8
#19: Protein 60S ribosomal protein L13


Mass: 24191.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S992
#20: Protein 60S ribosomal protein L14-like protein


Mass: 16111.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S1R0
#22: Protein 60S ribosomal protein L16-like protein


Mass: 23035.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SH61
#23: Protein 60S ribosomal protein l17-like protein


Mass: 21072.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SGY1
#26: Protein 60S ribosomal protein L20


Mass: 20341.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SCE2
#27: Protein 60S ribosomal protein l21-like protein


Mass: 18159.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S0Z3
#28: Protein 60S ribosomal protein L22-like protein


Mass: 14302.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SDS8
#29: Protein 60S ribosomal protein l23-like protein


Mass: 14674.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SI44
#30: Protein 60S ribosomal protein L24-like protein


Mass: 18081.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S1P9
#31: Protein 60S ribosomal protein L25-like protein


Mass: 17175.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S507
#32: Protein 60S ribosomal protein L26-like protein


Mass: 15565.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RYN9
#33: Protein 60S ribosomal protein L27


Mass: 15803.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RZE9
#34: Protein 60S ribosomal protein L28-like protein


Mass: 16848.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SGT6
#35: Protein 60S ribosomal protein L29


Mass: 7529.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: Q2H9W4
#36: Protein 60S ribosomal protein l30-like protein


Mass: 11602.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SEI0
#38: Protein 60S ribosomal protein L32-like protein


Mass: 15095.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S6V4
#39: Protein 60S ribosomal protein l33-like protein


Mass: 12330.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SCL3
#42: Protein 60S ribosomal protein L36


Mass: 12784.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SBN1
#44: Protein 60S ribosomal protein L38-like protein


Mass: 9537.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SG89
#47: Protein/peptide 60S ribosomal protein L41-A


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: P0CX86
#48: Protein 60S ribosomal protein L44-like protein


Mass: 12045.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SBZ6
#49: Protein 60S ribosomal protein L43-like protein


Mass: 10158.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S6B0

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Putative ribosomal ... , 2 types, 2 molecules LJSS

#17: Protein Putative ribosomal protein


Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SHQ2
#70: Protein Putative ribosomal protein


Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S6J7

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Ribosomal protein ... , 6 types, 6 molecules LNLQLRLgLjSb

#21: Protein Ribosomal protein L15


Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RZ88
#24: Protein Ribosomal protein L18-like protein


Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S9B5
#25: Protein Ribosomal protein L19


Mass: 22409.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S9T3
#40: Protein Ribosomal protein l34-like protein


Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SFN0
#43: Protein Ribosomal protein L37


Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S101
#79: Protein Ribosomal protein s27-like protein


Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S1S4

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Putative 60S ribosomal ... , 2 types, 2 molecules LdLq

#37: Protein Putative 60S ribosomal protein


Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SD68
#50: Protein Putative 60S ribosomal protein


Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SHJ6

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40S ribosomal protein ... , 29 types, 29 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSTSUSVSWSXSYSZSaScSeSf

#52: Protein 40S ribosomal protein S0


Mass: 31158.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RYF9
#53: Protein 40S ribosomal protein S1


Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S7T8
#54: Protein 40S ribosomal protein S2-like protein


Mass: 28556.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SAV4
#55: Protein 40S ribosomal protein S3-like protein


Mass: 27893.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S6I7
#56: Protein 40S ribosomal protein S4


Mass: 29800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S1A6
#57: Protein 40S ribosomal protein s5-like protein


Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S1Z0
#58: Protein 40S ribosomal protein S6


Mass: 27490.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RY43
#59: Protein 40S ribosomal protein S7


Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S8C4
#60: Protein 40S ribosomal protein S8


Mass: 23102.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RY45
#61: Protein 40S ribosomal protein s9-like protein


Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S0Z4
#62: Protein 40S ribosomal protein s10-like protein


Mass: 18121.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RZD8
#63: Protein 40S ribosomal protein S11-like protein


Mass: 18698.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SF00
#64: Protein 40S ribosomal protein S12


Mass: 15961.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SHH9
#65: Protein 40S ribosomal protein S13-like protein


Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RZM9
#66: Protein 40S ribosomal protein S14-like protein


Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SFL1
#67: Protein 40S ribosomal protein s15-like protein


Mass: 17601.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S084
#68: Protein 40S ribosomal protein S16-like protein


Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SBR7
#69: Protein 40S ribosomal protein S17-like protein


Mass: 16720.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S871
#71: Protein 40S ribosomal protein S19-like protein


Mass: 17151.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SFK8
#72: Protein 40S ribosomal protein S20-like protein


Mass: 13212.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S379
#73: Protein 40S ribosomal protein S21-like protein


Mass: 10961.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SI21
#74: Protein 40S ribosomal protein S22-like protein


Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SHI0
#75: Protein 40S ribosomal protein s23-like protein


Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0RY17
#76: Protein 40S ribosomal protein S24


Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: P0CU28
#77: Protein 40S ribosomal protein S25


Mass: 10932.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S1Y9
#78: Protein 40S ribosomal protein S26


Mass: 13616.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S2X4
#80: Protein 40S ribosomal protein S28-like protein


Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S9M9
#82: Protein 40S ribosomal protein S30


Mass: 6910.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: Q2H4C5
#83: Protein 40S ribosomal protein S27a-like protein


Mass: 17731.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S2X5

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Non-polymers , 3 types, 1524 molecules

#84: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 571 / Source method: obtained synthetically / Formula: Mg
#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#86: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 945 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chaetomium thermophilum 80S ribosome / Type: CELL / Entity ID: #1-#83 / Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 32.51 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19_4092refinement
PHENIX1.19_4092refinement
EM software
IDNameVersionCategory
2RELION3particle selection
8Cootmodel fitting
10RELION3CTF correction
11PHENIXmodel refinement
13RELION3initial Euler assignment
15cisTEMfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279818 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4V88

4v88

RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 136.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003220717
ELECTRON MICROSCOPYf_angle_d0.4405323303
ELECTRON MICROSCOPYf_chiral_restr0.031240284
ELECTRON MICROSCOPYf_plane_restr0.003621636
ELECTRON MICROSCOPYf_dihedral_angle_d13.158876024

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