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- PDB-9i1w: High resolution structure of the thermophilic 60S ribosomal subun... -

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Basic information

Entry
Database: PDB / ID: 9i1w
TitleHigh resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum
Components
  • (60S ribosomal protein ...) x 32
  • (Nascent chain ...) x 2
  • (Putative 60S ribosomal ...) x 2
  • (Putative ribosomal ...) x 2
  • (Ribosomal protein ...) x 6
  • 26S rRNA
  • 5.8S RNA
  • 5S RNA
  • 60S acidic ribosomal protein P0
  • Dolichyl-diphosphooligosaccharide--protein glycotransferase
  • E-site tRNA (5'-R(P*CP*CP*A)-3')
KeywordsRIBOSOME / 60S ribosomal subunit thermophilic eukaryote RNA modification pseudouridine
Function / homology
Function and homology information


regulation of cytoplasmic translational initiation / RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / oligosaccharyltransferase complex / preribosome / : / RNA polymerase I core promoter sequence-specific DNA binding / nucleolar large rRNA transcription by RNA polymerase I / ribosomal large subunit export from nucleus ...regulation of cytoplasmic translational initiation / RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / oligosaccharyltransferase complex / preribosome / : / RNA polymerase I core promoter sequence-specific DNA binding / nucleolar large rRNA transcription by RNA polymerase I / ribosomal large subunit export from nucleus / protein kinase activator activity / protein-RNA complex assembly / post-translational protein modification / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol
Similarity search - Function
Gcn1, N-terminal / : / : / : / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Stalled ribosome sensor GCN1-like, HEAT repeats / Fungal GCN1-like, HEAT repeats / Stalled ribosome sensor GCN1 N-terminal / Stalled ribosome sensor GCN1-like, HEAT repeats / Transcription initiation factor Rrn7, Zinc-finger ...Gcn1, N-terminal / : / : / : / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Stalled ribosome sensor GCN1-like, HEAT repeats / Fungal GCN1-like, HEAT repeats / Stalled ribosome sensor GCN1 N-terminal / Stalled ribosome sensor GCN1-like, HEAT repeats / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / : / : / 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 / Elongation factor 3/GNC1 HEAT repeat / EF3 N-terminal HEAT repeat / Centrosomal protein CEP104-like, TOG domain / : / STT3/PglB/AglB core domain / Parkin co-regulated protein / TOG domain / Parkin co-regulated protein / TOG / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / : / : / HEAT repeat profile. / HEAT, type 2 / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Ribosomal protein L30e / Ribosomal protein L28e / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e signature. / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / : / Ribosomal L40e family / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / : / Ribosomal Protein L6, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site
Similarity search - Domain/homology
: / SPERMIDINE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / 60S ribosomal protein L26-like protein / Ribosomal protein L15 ...: / SPERMIDINE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / 60S ribosomal protein L26-like protein / Ribosomal protein L15 / 60S ribosomal protein L27 / 60S ribosomal protein L6 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 / 60S ribosomal protein l9-like protein / 60S ribosomal protein l21-like protein / Ribosomal protein L37 / 60S ribosomal protein L24-like protein / 60S ribosomal protein L14-like protein / 60S ribosomal protein L2-like protein / 60S ribosomal protein L25-like protein / 60S ribosomal protein L43-like protein / 60S ribosomal protein L32-like protein / Putative ribosomal protein / 60S ribosomal protein L13 / Ribosomal protein L18-like protein / Ribosomal protein L19 / 60S ribosomal protein L8 / 60S ribosomal protein L36 / 60S ribosomal protein L44-like protein / 60S ribosomal protein L20 / 60S ribosomal protein l33-like protein / 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 / 60S ribosomal protein L4-like protein / 60S ribosomal protein l7-like protein / Ribosomal protein l34-like protein / 60S ribosomal protein L38-like protein / 60S ribosomal protein L12-like protein / 60S acidic ribosomal protein P0 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L16-like protein / Putative 60S ribosomal protein / Large ribosomal subunit protein uL5 / 60S ribosomal protein l23-like protein / Small ribosomal subunit protein eS32A
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsWild, K. / Klein, M.A. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Pseudouridine increases ribosome stability in a thermophilic eukaryote.
Authors: Klemens Wild / Marius Klein / Alicia Burkard / Virginie Marchand / Nikola Kellner / Antonio Paez / Stefan Pastore / Tamer Butto / Yuri Motorin / Mark Helm / Irmgard Sinning /
Abstract: RNA modifications alter stability, folding space, and interaction network of RNA molecules. Ribosomal RNA (rRNA) modifications stabilize the structure of ribosomes and cluster around functionally ...RNA modifications alter stability, folding space, and interaction network of RNA molecules. Ribosomal RNA (rRNA) modifications stabilize the structure of ribosomes and cluster around functionally important sites such as the peptidyl transferase center, ribosomal subunit bridges, and the polypeptide tunnel. Here, we investigate the rRNA modifications of the thermophilic fungus Chaetomium thermophilum (ct), a model organism for eukaryotic thermophily and structural stability. Using LC-MS/MS, orthogonal second and third generation RNA-sequencing and high-resolution cryo-electron microscopy, we describe a cross-correlating method to assign and quantify all ct rRNA modifications. Overall, a doubling of rRNA modifications to 4% explains ribosomal thermostability with an extended distribution towards peripheral functional sites. The 2.4 Å structure of the idle ct60S ribosome, retaining nascent chains and including metal ions, polyamines, and water molecules, allows for a comprehensive structure-function analysis. Comparison with mesophilic ribosomes from Chaetomium globosum, yeast, and human highlights the significant increase of pseudouridines (Ψs). The number of Ψs linearly correlates with growth temperature, suggesting statistical modification. A ct-specific Ψ substitution forming a 'Ψ-turn' at the polypeptide tunnel exit close to the third constriction exemplifies mechanistic adaptations of the ribosome at elevated temperatures.
History
DepositionJan 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: 26S rRNA
3: 5S RNA
4: 5.8S RNA
9: E-site tRNA (5'-R(P*CP*CP*A)-3')
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: Ribosomal protein eL39
Lm: Putative ribosomal protein
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
PC: Nascent chain C-terminus
PN: Nascent chain N-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,037,187487
Polymers2,023,00651
Non-polymers14,182436
Water40,6422256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 4 molecules 1349

#1: RNA chain 26S rRNA


Mass: 1079529.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#2: RNA chain 5S RNA


Mass: 38612.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#3: RNA chain 5.8S RNA


Mass: 50161.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#4: RNA chain E-site tRNA (5'-R(P*CP*CP*A)-3')


Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)

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

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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 22888.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SH61
#20: Protein 60S ribosomal protein l17-like protein


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


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


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


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


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


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


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


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


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


Mass: 16848.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#32: Protein 60S ribosomal protein L29


Mass: 15041.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#33: Protein 60S ribosomal protein l30-like protein


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


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


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


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


Mass: 9537.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SG89
#44: Protein/peptide 60S ribosomal protein L41-A / Ribosomal protein eL41


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


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


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

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Putative ribosomal ... , 2 types, 2 molecules LJLm

#14: Protein Putative ribosomal protein


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


Mass: 14609.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S8G4

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Ribosomal protein ... , 6 types, 6 molecules LNLQLRLgLjLl

#18: Protein Ribosomal protein L15


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


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


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


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


Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S101
#42: Protein Ribosomal protein eL39


Mass: 12577.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)

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

#34: Protein Putative 60S ribosomal protein


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


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

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Protein , 2 types, 2 molecules LhLs

#38: Protein Dolichyl-diphosphooligosaccharide--protein glycotransferase


Mass: 14643.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase
#48: Protein 60S acidic ribosomal protein P0


Mass: 33853.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SGP3

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Nascent chain ... , 2 types, 2 molecules PCPN

#49: Protein/peptide Nascent chain C-terminus


Mass: 188.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#50: Protein/peptide Nascent chain N-terminus


Mass: 528.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)

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Non-polymers , 6 types, 2692 molecules

#51: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#52: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#53: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 239 / Source method: obtained synthetically / Formula: Mg
#54: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 188 / Source method: obtained synthetically / Formula: K
#55: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#56: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2256 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 60S subunit / Type: RIBOSOME / Entity ID: #1-#50 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Thermochaetoides thermophila (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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 42.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 653542 / Symmetry type: POINT

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