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- PDB-7z3n: Cryo-EM structure of the ribosome-associated RAC complex on the 8... -

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Basic information

Entry
Database: PDB / ID: 7z3n
TitleCryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-1 conformation
Components
  • (40S ribosomal protein ...) x 29
  • (60S ribosomal protein ...) x 29
  • (Putative 60S ribosomal ...) x 2
  • (Putative ribosomal ...) x 3
  • (Ribosomal protein ...) x 8
  • 18S rRNA
  • 26S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • Dolichyl-diphosphooligosaccharide--protein glycotransferase
  • HABP4_PAI-RBP1 domain-containing protein
  • Nascent chain
  • Putative guanine nucleotide-binding protein
  • Putative heat shock protein
  • Putative ribosome associated protein
  • eL24
  • eL38
  • uL6
KeywordsCHAPERONE / RAC / ribosome-associated complex / thermophilic eukaryotic ribosome / 80S
Function / homology
Function and homology information


RNA polymerase I core factor complex / 'de novo' cotranslational protein folding / 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 / 90S preribosome / regulation of translational fidelity ...RNA polymerase I core factor complex / 'de novo' cotranslational protein folding / 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 / 90S preribosome / regulation of translational fidelity / translation regulator activity / Hsp70 protein binding / 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 / ribosome biogenesis / large ribosomal subunit / regulation of translation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / methylation / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / : / Ribosome-associated complex head domain / Zuotin-like, zuotin homology domain / Gcn1, N-terminal / : / : / Generalcontrol nonderepressible 1 (Gcn1) N-terminal ...Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / : / Ribosome-associated complex head domain / Zuotin-like, zuotin homology domain / 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 / 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 / Elongation factor 3/GNC1 HEAT repeat / EF3 N-terminal HEAT 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 / DnaJ domain / HEAT repeat profile. / HEAT, type 2 / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Heat shock protein 70 family / Hsp70 protein / : / 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 S26e signature. / 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 L13e, conserved site / Ribosomal protein L13e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / S27a-like superfamily / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / : / 60S ribosomal protein L18a/ L20, eukaryotes
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / Putative ribosome associated protein ...ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / Putative ribosome associated protein / 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 / Putative heat shock protein / 40S ribosomal protein s15-like protein / 60S ribosomal protein L6 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 / 60S ribosomal protein l21-like protein / 40S ribosomal protein s9-like protein / Ribosomal protein L37 / 40S ribosomal protein S4 / 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 / 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 L12-like protein / 60S acidic ribosomal protein P0 / Large ribosomal subunit protein uL22 / 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
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKisonaite, M. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structural inventory of cotranslational protein folding by the eukaryotic RAC complex.
Authors: Miglė Kišonaitė / Klemens Wild / Karine Lapouge / Genís Valentín Gesé / Nikola Kellner / Ed Hurt / Irmgard Sinning /
Abstract: The challenge of nascent chain folding at the ribosome is met by the conserved ribosome-associated complex (RAC), which forms a chaperone triad with the Hsp70 protein Ssb in fungi, and consists of ...The challenge of nascent chain folding at the ribosome is met by the conserved ribosome-associated complex (RAC), which forms a chaperone triad with the Hsp70 protein Ssb in fungi, and consists of the non-canonical Hsp70 Ssz1 and the J domain protein Zuotin (Zuo1). Here we determine cryo-EM structures of Chaetomium thermophilum RAC bound to 80S ribosomes. RAC adopts two distinct conformations accommodating continuous ribosomal rotation by a flexible lever arm. It is held together by a tight interaction between the Ssz1 substrate-binding domain and the Zuo1 N terminus, and additional contacts between the Ssz1 nucleotide-binding domain and Zuo1 J- and Zuo1 homology domains, which form a rigid unit. The Zuo1 HPD motif conserved in J-proteins is masked in a non-canonical interaction by the Ssz1 nucleotide-binding domain, and allows the positioning of Ssb for activation by Zuo1. Overall, we provide the basis for understanding how RAC cooperates with Ssb in a dynamic nascent chain interaction and protein folding.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 3, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_label_asym_id
Revision 1.3May 31, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Putative ribosome associated protein
D: Putative heat shock protein
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: uL6
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: eL24
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: eL38
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
NC: Nascent chain
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: Ribosomal protein uS14
Se: 40S ribosomal protein S30
Sf: 40S ribosomal protein S27a-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,361,393550
Polymers3,349,30486
Non-polymers12,089464
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "Ln"
d_2ens_1chain "Lr"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METSERVA1 - 24
d_21ens_1METSERZA1 - 24

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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) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#2: RNA chain 18S rRNA


Mass: 578772.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#3: RNA chain 5S rRNA


Mass: 38596.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#4: RNA chain 5.8S rRNA


Mass: 50147.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719

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Protein , 9 types, 9 molecules ABCDLHLWLhLkLs

#5: Protein Putative guanine nucleotide-binding protein


Mass: 35149.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / 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) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S428
#7: Protein Putative ribosome associated protein


Mass: 51048.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYD6
#8: Protein Putative heat shock protein


Mass: 62449.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZX9
#16: Protein uL6


Mass: 21582.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#31: Protein eL24


Mass: 18081.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#42: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase
#45: Protein eL38


Mass: 9537.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#52: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGP3

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60S ribosomal protein ... , 29 types, 30 molecules LALBLCLDLELFLGLILKLLLMLOLPLSLTLULVLXLYLZLaLbLcLeLfLiLnLrLoLp

#9: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4P8
#10: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXW1
#11: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFC3
#12: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEG2
#13: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0D6
#14: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFL0
#15: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAJ9
#17: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEI1
#19: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGH8
#20: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S992
#21: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1R0
#23: Protein 60S ribosomal protein L16-like protein


Mass: 23035.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SH61
#24: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGY1
#27: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCE2
#28: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0Z3
#29: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SDS8
#30: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SI44
#32: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S507
#33: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYN9
#34: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZE9
#35: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#36: Protein 60S ribosomal protein L29


Mass: 7529.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#37: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEI0
#39: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6V4
#40: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCL3
#43: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBN1
#48: Protein/peptide 60S ribosomal protein L41-A


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#49: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBZ6
#50: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6B0

-
Putative ribosomal ... , 3 types, 3 molecules LJLmSS

#18: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHQ2
#47: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8G4
#72: Protein Putative ribosomal protein


Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6J7

-
Ribosomal protein ... , 8 types, 8 molecules LNLQLRLgLjLlSbSd

#22: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZ88
#25: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9B5
#26: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9T3
#41: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFN0
#44: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S101
#46: Protein Ribosomal protein eL39


Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#81: Protein Ribosomal protein s27-like protein


Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1S4
#83: Protein Ribosomal protein uS14


Mass: 6504.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719

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

#38: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SD68
#51: 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHJ6

-
Protein/peptide , 1 types, 1 molecules NC

#53: Protein/peptide Nascent chain


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719

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

#54: Protein 40S ribosomal protein S0


Mass: 31158.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYF9
#55: Protein 40S ribosomal protein S1


Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S7T8
#56: Protein 40S ribosomal protein S2-like protein


Mass: 28556.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAV4
#57: Protein 40S ribosomal protein S3-like protein


Mass: 27893.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6I7
#58: Protein 40S ribosomal protein S4


Mass: 29800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1A6
#59: Protein 40S ribosomal protein s5-like protein


Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1Z0
#60: Protein 40S ribosomal protein S6


Mass: 27490.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RY43
#61: Protein 40S ribosomal protein S7


Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8C4
#62: Protein 40S ribosomal protein S8


Mass: 23102.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RY45
#63: Protein 40S ribosomal protein s9-like protein


Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0Z4
#64: Protein 40S ribosomal protein s10-like protein


Mass: 18121.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZD8
#65: Protein 40S ribosomal protein S11-like protein


Mass: 18698.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SF00
#66: Protein 40S ribosomal protein S12


Mass: 15961.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHH9
#67: Protein 40S ribosomal protein S13-like protein


Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZM9
#68: Protein 40S ribosomal protein S14-like protein


Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFL1
#69: Protein 40S ribosomal protein s15-like protein


Mass: 17601.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S084
#70: Protein 40S ribosomal protein S16-like protein


Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBR7
#71: Protein 40S ribosomal protein S17-like protein


Mass: 16720.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S871
#73: Protein 40S ribosomal protein S19-like protein


Mass: 17151.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFK8
#74: Protein 40S ribosomal protein S20-like protein


Mass: 13212.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S379
#75: Protein 40S ribosomal protein S21-like protein


Mass: 10961.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SI21
#76: Protein 40S ribosomal protein S22-like protein


Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHI0
#77: Protein 40S ribosomal protein s23-like protein


Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RY17
#78: Protein 40S ribosomal protein S24


Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: P0CU28
#79: Protein 40S ribosomal protein S25


Mass: 10932.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1Y9
#80: Protein 40S ribosomal protein S26


Mass: 13616.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S2X4
#82: Protein 40S ribosomal protein S28-like protein


Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9M9
#84: Protein 40S ribosomal protein S30


Mass: 6910.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#85: Protein 40S ribosomal protein S27a-like protein


Mass: 17731.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S2X5

-
Non-polymers , 3 types, 464 molecules

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


Mass: 24.305 Da / Num. of mol.: 455 / Source method: obtained synthetically / Formula: Mg
#87: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#88: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Chaetomium thermophilum RAC on 80S ribosome / Type: COMPLEX / Entity ID: #1-#85 / 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

-
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: 39.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.19_4092refinement
PHENIX1.19_4092refinement
EM software
IDNameVersionCategory
2RELION3particle selection
8Cootmodel fitting
10RELION3CTF correction
12RELION3initial Euler assignment
14cisTEMfinal Euler assignment
17PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305951 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7OLC

7olc

RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 201.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029228110
ELECTRON MICROSCOPYf_angle_d0.6845333340
ELECTRON MICROSCOPYf_chiral_restr0.039941427
ELECTRON MICROSCOPYf_plane_restr0.006522928
ELECTRON MICROSCOPYf_dihedral_angle_d13.855277117
Refine LS restraints NCSType: NCS constraints / Rms dev position: 0.000700055497955 Å

+
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