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- PDB-8i9p: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal ... -

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Entry
Database: PDB / ID: 8i9p
TitleCryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16
Components
  • (60S ribosomal protein ...) x 15
  • (Brix domain-containing ...) x 2
  • (Ribosomal protein ...) x 3
  • (Ribosome biogenesis protein ...) x 2
  • Nucleolar protein 16
  • Pescadillo homolog
  • Protein MAK16
  • Putative RNA-binding protein
  • RNA (306-MER)
  • RNA (3341-MER)
  • RNA helicase
  • Ribosomal RNA-processing protein 1
  • dolichyl-diphosphooligosaccharide--protein glycotransferase
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / Ribosome biogenesis / pre-60S ribosome
Function / homology
Function and homology information


dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / PeBoW complex / rRNA primary transcript binding / 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 / preribosome, large subunit precursor / ribonucleoprotein complex binding ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / PeBoW complex / rRNA primary transcript binding / 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 / preribosome, large subunit precursor / ribonucleoprotein complex binding / maturation of LSU-rRNA / endomembrane system / post-translational protein modification / nuclear periphery / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / ribosome biogenesis / large ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / negative regulation of translation / rRNA binding / structural constituent of ribosome / RNA helicase / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane
Similarity search - Function
Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / : / STT3/PglB/AglB core domain / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain ...Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / : / STT3/PglB/AglB core domain / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Domain of unknown function DUF4217 / : / ATP-dependent rRNA helicase SPB4-like, C-terminal extension / DUF4217 / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / U3 snoRNP protein/Ribosome production factor 1 / Pescadillo / Pescadillo N-terminus / Brix domain / Brix domain / Brix domain profile. / Brix / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / BRCA1 C Terminus (BRCT) domain / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / BRCT domain profile. / 60S ribosomal protein L18a/ L20, eukaryotes / BRCT domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / BRCT domain superfamily / Ribosomal Protein L6, KOW domain / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L6e / 60S ribosomal protein L6E / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L14 / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Brix domain-containing protein / 60S ribosomal protein L26-like protein / ATP-dependent RNA helicase / Ribosomal protein L15 / 60S ribosomal protein L6 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Brix domain-containing protein / 60S ribosomal protein L26-like protein / ATP-dependent RNA helicase / Ribosomal protein L15 / 60S ribosomal protein L6 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 / 60S ribosomal protein l21-like protein / Ribosomal protein L37 / Putative RNA-binding protein / 60S ribosomal protein L14-like protein / Ribosomal RNA-processing protein 1 / Brix domain-containing protein / 60S ribosomal protein L25-like protein / 60S ribosomal protein L32-like protein / Uncharacterized protein / Nucleolar protein 16 / 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 / 60S ribosomal protein L4-like protein / Protein MAK16 / 60S ribosomal protein l7-like protein / rRNA processing protein / Large ribosomal subunit protein uL22 / 60S ribosomal protein L16-like protein / Pescadillo homolog
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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 (306-MER)
CA: Brix domain-containing protein
CB: Ribosome biogenesis protein C8F11.04
CC: Ribosome biogenesis protein ERB1
CE: RNA helicase
CI: Putative RNA-binding protein
CJ: Pescadillo homolog
CM: 60S ribosomal protein l7-like protein
CR: Nucleolar protein 16
CU: rRNA-processing protein EBP2
LC: 60S ribosomal protein L4-like protein
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein l7-like protein
LG: 60S ribosomal protein L8
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
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
Cc: Ribosomal RNA-processing protein 1
Cd: Brix domain-containing protein
Ce: Protein MAK16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,246,93035
Polymers2,246,79933
Non-polymers1312
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 , 2 types, 2 molecules C1C2

#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 (306-MER)


Mass: 98523.078 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 / References: GenBank: 261599337

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Brix domain-containing ... , 2 types, 2 molecules CACd

#3: 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
#31: 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

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Ribosome biogenesis protein ... , 2 types, 2 molecules CBCC

#4: 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
#5: 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

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Protein , 8 types, 8 molecules CECICJCRCULhCcCe

#6: 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
#7: 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
#8: 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
#10: 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
#11: 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
#27: 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
#30: 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
#32: 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 ribosomal protein ... , 15 types, 16 molecules CMLFLCLELGLLLMLOLPLSLTLXLYLeLfLi

#9: 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
#12: 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
#13: 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
#14: Protein 60S ribosomal protein L8


Mass: 29744.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAJ9
#15: 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
#16: 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
#18: 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
#19: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#28: 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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Ribosomal protein ... , 3 types, 3 molecules LNLQLj

#17: 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
#20: 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
#29: 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 , 1 types, 2 molecules

#33: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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-#320NATURAL
2ribosomeRIBOSOME#1-#321NATURAL
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 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83243 / Symmetry type: POINT

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