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- PDB-8i9t: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal ... -

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Basic information

Entry
Database: PDB / ID: 8i9t
TitleCryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1
Components
  • (60S ribosomal protein ...) x 19
  • (60S ribosome ...) x 2
  • (Brix domain-containing ...) x 3
  • (Ribosomal RNA-processing protein ...) x 2
  • (Ribosomal protein ...) x 3
  • (Ribosome biogenesis protein ...) x 4
  • (rRNA-processing ...) x 2
  • 60S ribosomal subunit-like protein
  • ATP-dependent RNA helicase DBP10
  • AdoMet-dependent rRNA methyltransferase SPB1
  • DUF2423 domain-containing protein
  • Eukaryotic translation initiation factor 6
  • Nucleolar GTP-binding protein 1
  • Nucleolar protein 16
  • Pescadillo homolog
  • Protein MAK16
  • Putative GTP binding protein
  • Putative RNA-binding protein
  • RNA (161-MER)
  • RNA (256-MER)
  • RNA (3341-MER)
  • RNA helicase
  • RNA methyltransferase nop2-like protein
  • Ribosomal protein
  • Ribosome assembly factor mrt4
  • dolichyl-diphosphooligosaccharide--protein glycotransferase
KeywordsRIBOSOME / Ribosome biogenesis / pre-60S ribosome
Function / homology
Function and homology information


dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine / PeBoW complex / rRNA primary transcript binding / rRNA base methylation ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine / PeBoW complex / rRNA primary transcript binding / rRNA base methylation / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / preribosome, small subunit precursor / ribosomal large subunit binding / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / mRNA transport / ribosomal subunit export from nucleus / ribonucleoprotein complex binding / maturation of LSU-rRNA / translation initiation factor activity / endomembrane system / post-translational protein modification / nuclear periphery / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / ribosomal large subunit biogenesis / cytosolic ribosome assembly / rRNA processing / ribosome biogenesis / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / gene expression / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / negative regulation of translation / rRNA binding / RNA helicase / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal RNA-processing protein 14, N-terminal / 60S ribosome biogenesis protein Rrp14 / Ribosomal RNA-processing protein 15 / Protein Peter Pan-like / Rrp15p / Surfeit locus 6 / Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domain / Surfeit locus protein 6 / DBP10, C-terminal / DDX54/DBP10 family ...Ribosomal RNA-processing protein 14, N-terminal / 60S ribosome biogenesis protein Rrp14 / Ribosomal RNA-processing protein 15 / Protein Peter Pan-like / Rrp15p / Surfeit locus 6 / Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domain / Surfeit locus protein 6 / DBP10, C-terminal / DDX54/DBP10 family / DBP10CT (NUC160) domain / DBP10CT (NUC160) domain / 60S ribosomal subunit assembly/export protein Loc1 / : / Methyltr_RsmF/B-like, ferredoxin-like domain / Ribosome biogenesis factor, NIP7 / RNA (C5-cytosine) methyltransferase, NOP2 / : / Ribosomal RNA processing protein 1-like / UPF0113, pre-PUA domain / UPF0113 PUA domain / Nucleolar protein,Nop52 / NIP7/UPF0113, pre-PUA domain / UPF0113, PUA domain / Mak16 protein / Nop2p / Mak16 protein C-terminal region / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / : / STT3/PglB/AglB core domain / Ribosomal RNA methyltransferase, SPB1-like, C-terminal / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / AdoMet-dependent rRNA methyltransferase SPB1-like / Spb1 C-terminal domain / Ribosomal RNA methyltransferase Spb1, DUF3381 / Cgr1-like / Cgr1 family / : / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / : / Ribosomal RNA large subunit methyltransferase E / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / : / Oligosaccharyl transferase, STT3 subunit / Domain of unknown function DUF4217 / Oligosaccharyl transferase STT3, N-terminal / ATP-dependent rRNA helicase SPB4-like, C-terminal extension / DUF4217 / Domain of unknown function DUF2423 / YBL028C ribosome biogenesis factor, N-terminal domain / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / : / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / Guanine nucleotide-binding protein-like 3, N-terminal domain / GNL3L/Grn1 putative GTPase / U3 snoRNP protein/Ribosome production factor 1 / PUA domain / PUA domain superfamily / PUA domain profile. / : / Pescadillo / Pescadillo N-terminus / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal biogenesis NSA2 family / Ribosome assembly factor Mrt4 / : / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / Brix domain / Brix domain / Brix domain profile. / Brix / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / 50S ribosome-binding GTPase / RNA helicase, DEAD-box type, Q motif
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Brix domain-containing protein / 60S ribosomal protein L26-like protein / ATP-dependent RNA helicase / Ribosomal protein L15 ...GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Brix domain-containing protein / 60S ribosomal protein L26-like protein / ATP-dependent RNA helicase / Ribosomal protein L15 / Ribosome biogenesis protein NSA2 homolog / 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 / Putative RNA-binding protein / 60S ribosomal protein L14-like protein / Uncharacterized protein / 60S ribosome subunit biogenesis protein NIP7 / Ribosome biogenesis protein RLP24 / Ribosomal RNA-processing protein 1 / Brix domain-containing protein / Ribosomal protein / 60S ribosomal protein L25-like protein / Ribosomal RNA-processing protein 15 / RNA helicase / Large ribosomal subunit protein uL10 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L32-like protein / Brix domain-containing protein / Uncharacterized protein / Nucleolar protein 16 / Nucleolar GTP-binding protein 1 / 60S ribosomal protein L13 / Ribosomal protein L18-like protein / 60S ribosomal protein L8 / 60S ribosomal protein L36 / 60S ribosomal protein L20 / Ribosome biogenesis protein ERB1 / 60S ribosomal protein l33-like protein / rRNA-processing protein / Putative GTP binding protein / 60S ribosomal protein L4-like protein / Protein MAK16 / 60S ribosomal protein l7-like protein / rRNA processing protein / Uncharacterized protein / 60S ribosomal protein L12-like protein / 60S ribosomal subunit-like protein / Large ribosomal subunit protein uL22 / 60S ribosomal protein L16-like protein / DUF2423 domain-containing protein / RNA methyltransferase nop2-like protein / Pescadillo homolog / 60S ribosomal protein l23-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLau, B. / Huang, Z. / Beckmann, R. / Hurt, E. / Cheng, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: EMBO Rep / Year: 2023
Title: Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
Authors: Benjamin Lau / Zixuan Huang / Nikola Kellner / Shuangshuang Niu / Otto Berninghausen / Roland Beckmann / Ed Hurt / Jingdong Cheng /
Abstract: Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ...Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.
History
DepositionFeb 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C1: RNA (3341-MER)
C2: RNA (256-MER)
C3: RNA (161-MER)
CA: Brix domain-containing protein
CB: Ribosome biogenesis protein C8F11.04
CC: Ribosome biogenesis protein ERB1
CE: RNA helicase
CF: Ribosome assembly factor mrt4
CG: 60S ribosome subunit biogenesis protein NIP7
CH: Nucleolar GTP-binding protein 1
CI: Putative RNA-binding protein
CJ: Pescadillo homolog
CK: Ribosome biogenesis protein NSA2 homolog
CL: Putative GTP binding protein
CM: 60S ribosomal protein l7-like protein
CN: Eukaryotic translation initiation factor 6
CO: DUF2423 domain-containing protein
CP: RNA methyltransferase nop2-like protein
CQ: Ribosome biogenesis protein RLP24
CR: Nucleolar protein 16
CS: AdoMet-dependent rRNA methyltransferase SPB1
CU: rRNA-processing protein EBP2
CX: 60S ribosomal subunit-like protein
Cz: rRNA-processing protein
Cb: ATP-dependent RNA helicase DBP10
Ch: Ribosomal RNA-processing protein 15
LB: 60S ribosomal protein L3-like protein
LC: 60S ribosomal protein L4-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
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
LS: 60S ribosomal protein L20
LT: 60S ribosomal protein l21-like protein
LV: 60S ribosomal protein l23-like protein
LX: 60S ribosomal protein L25-like protein
LY: 60S ribosomal protein L26-like protein
Le: 60S ribosomal protein L32-like protein
Lf: 60S ribosomal protein l33-like protein
Lh: dolichyl-diphosphooligosaccharide--protein glycotransferase
Li: 60S ribosomal protein L36
Lj: Ribosomal protein L37
Lq: Ribosomal protein
Cc: Ribosomal RNA-processing protein 1
Cd: Brix domain-containing protein
Ce: Protein MAK16
Cf: 60S ribosome biogenesis protein Rrp14
Cg: Brix domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,133,10359
Polymers3,132,38355
Non-polymers7194
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules C1C2C3

#1: RNA chain RNA (3341-MER)


Mass: 1079977.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 25S rRNA / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
#2: RNA chain RNA (256-MER)


Mass: 82467.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 5.8S rRNA / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
#3: RNA chain RNA (161-MER)


Mass: 51802.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ITS2 rRNA / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719

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Brix domain-containing ... , 3 types, 3 molecules CACdCg

#4: Protein Brix domain-containing protein


Mass: 36482.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXZ3
#51: Protein Brix domain-containing protein


Mass: 49471.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4S2
#54: Protein Brix domain-containing protein


Mass: 54249.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S732

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Ribosome biogenesis protein ... , 4 types, 4 molecules CBCCCKCQ

#5: Protein Ribosome biogenesis protein C8F11.04


Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S7X0
#6: Protein Ribosome biogenesis protein ERB1 / Eukaryotic ribosome biogenesis protein 1


Mass: 90838.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCK6
#13: Protein Ribosome biogenesis protein NSA2 homolog


Mass: 29724.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S081
#19: Protein Ribosome biogenesis protein RLP24


Mass: 26434.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S497

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Protein , 16 types, 16 molecules CECFCHCICJCLCNCOCPCRCSCXCbLhLqCe

#7: Protein RNA helicase


Mass: 66830.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYU9
#8: Protein Ribosome assembly factor mrt4 / mRNA turnover protein 4


Mass: 30551.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S616
#10: Protein Nucleolar GTP-binding protein 1


Mass: 75621.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8F1
#11: Protein Putative RNA-binding protein


Mass: 45884.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1H0
#12: Protein Pescadillo homolog / Nucleolar protein 7 homolog


Mass: 77167.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHX6
#14: Protein Putative GTP binding protein


Mass: 61523.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEW3
#16: Protein Eukaryotic translation initiation factor 6


Mass: 26468.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S683
#17: Protein DUF2423 domain-containing protein


Mass: 13262.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHK0
#18: Protein RNA methyltransferase nop2-like protein


Mass: 83658.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHQ0
#20: Protein Nucleolar protein 16


Mass: 26960.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S832
#21: Protein AdoMet-dependent rRNA methyltransferase SPB1 / 2'-O-ribose RNA methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase


Mass: 83181.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G0SGD8, Transferases; Transferring one-carbon groups; Methyltransferases
#23: Protein 60S ribosomal subunit-like protein


Mass: 22678.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGJ0
#25: Protein ATP-dependent RNA helicase DBP10


Mass: 81734.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5S8, RNA helicase
#46: Protein dolichyl-diphosphooligosaccharide--protein glycotransferase


Mass: 105169.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase
#49: Protein Ribosomal protein


Mass: 24055.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4Z9
#52: Protein Protein MAK16


Mass: 39464.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFD6

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60S ribosome ... , 2 types, 2 molecules CGCf

#9: Protein 60S ribosome subunit biogenesis protein NIP7


Mass: 20685.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S435
#53: Protein 60S ribosome biogenesis protein Rrp14


Mass: 64465.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S2I7

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60S ribosomal protein ... , 19 types, 20 molecules CMLFLBLCLELGLHLKLLLMLOLPLSLTLVLXLYLeLfLi

#15: Protein 60S ribosomal protein l7-like protein


Mass: 28821.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFL0
#27: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXW1
#28: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFC3
#29: Protein 60S ribosomal protein L6


Mass: 22132.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0D6
#30: Protein 60S ribosomal protein L8


Mass: 29744.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAJ9
#31: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0E5
#32: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGH8
#33: Protein 60S ribosomal protein L13


Mass: 24191.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S992
#34: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1R0
#36: Protein 60S ribosomal protein L16-like protein


Mass: 22993.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SH61
#37: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGY1
#39: Protein 60S ribosomal protein L20


Mass: 20341.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCE2
#40: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0Z3
#41: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SI44
#42: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S507
#43: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYN9
#44: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6V4
#45: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCL3
#47: Protein 60S ribosomal protein L36


Mass: 12784.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBN1

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RRNA-processing ... , 2 types, 2 molecules CUCz

#22: Protein rRNA-processing protein EBP2


Mass: 50255.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGC2
#24: Protein rRNA-processing protein


Mass: 14710.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCP3

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Ribosomal RNA-processing protein ... , 2 types, 2 molecules ChCc

#26: Protein Ribosomal RNA-processing protein 15


Mass: 38314.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5P7
#50: Protein Ribosomal RNA-processing protein 1


Mass: 32128.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4M2

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Ribosomal protein ... , 3 types, 3 molecules LNLQLj

#35: Protein Ribosomal protein L15


Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZ88
#38: 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 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9B5
#48: Protein Ribosomal protein L37


Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S101

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Non-polymers , 2 types, 4 molecules

#55: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#56: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1pre-60S ribosomeRIBOSOME#1-#470NATURAL
2ribosomeRIBOSOME#1-#471NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Chaetomium thermophilum (fungus)759272
32Chaetomium thermophilum (fungus)759272
Buffer solutionpH: 7.4
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 / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52677 / Symmetry type: POINT

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