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- PDB-7ohq: Nog1-TAP associated immature ribosomal particle population C from... -

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Basic information

Entry
Database: PDB / ID: 7ohq
TitleNog1-TAP associated immature ribosomal particle population C from S. cerevisiae
Components
  • (60S ribosomal protein ...) x 35
  • (Nucleolar GTP-binding protein ...) x 2
  • (Ribosome assembly ...) x 2
  • (Ribosome biogenesis protein ...) x 6
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • Eukaryotic translation initiation factor 6
  • ITS2
  • Nuclear GTP-binding protein NUG1
  • Pescadillo homolog
  • Proteasome-interacting protein CIC1
  • Regulator of ribosome biosynthesis
  • UPF0642 protein YBL028C
  • rRNA-processing protein CGR1
KeywordsRIBOSOME / ribosomal assembly state
Function / homology
Function and homology information


protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / PeBoW complex / 7S RNA binding / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / PeBoW complex / 7S RNA binding / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / hexon binding / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome complex / nuclear periphery / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cytosolic ribosome assembly / small-subunit processome / macroautophagy / maintenance of translational fidelity / protein catabolic process / rRNA processing / protein transport / ribosome biogenesis / viral capsid / protein-macromolecule adaptor activity / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / host cell nucleus / GTP binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosome biogenesis protein Rpf2 / Ribosome biogenesis protein 15, RNA recognition motif / Ribosome biogenesis protein Nop53/GLTSCR2 / Nop53 (60S ribosomal biogenesis) / Cgr1-like / Cgr1 family / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 ...Ribosome biogenesis protein Rpf2 / Ribosome biogenesis protein 15, RNA recognition motif / Ribosome biogenesis protein Nop53/GLTSCR2 / Nop53 (60S ribosomal biogenesis) / Cgr1-like / Cgr1 family / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain / Domain of unknown function DUF2423 / YBL028C ribosome biogenesis factor, N-terminal domain / NLE / NLE (NUC135) domain / Guanine nucleotide-binding protein-like 3, N-terminal domain / GNL3L/Grn1 putative GTPase / : / Pescadillo / Pescadillo N-terminus / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal biogenesis NSA2 family / Ribosome assembly factor Mrt4 / : / BRCT domain, a BRCA1 C-terminus domain / 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 / 50S ribosome-binding GTPase / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / GTP binding domain / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / breast cancer carboxy-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L14e domain / Ribosomal protein L35Ae, conserved site / 60S ribosomal protein L19 / Ribosomal protein L14 / Ribosomal protein L35Ae signature. / Ribosomal protein L30/YlxQ / Ribosomal Protein L6, KOW domain
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Pre-hexon-linking protein VIII / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Ribosome assembly protein 4 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL13A / Ribosome assembly factor MRT4 / Large ribosomal subunit protein eL14A / Ribosome biogenesis protein RPF2 / Large ribosomal subunit protein eL32 / UPF0642 protein YBL028C / Proteasome-interacting protein CIC1 / Nuclear GTP-binding protein NUG1 / Ribosome biogenesis protein NSA2 / Ribosome biogenesis protein RLP7 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / rRNA-processing protein CGR1 / Pescadillo homolog / Nucleolar GTP-binding protein 2 / Ribosome biogenesis protein 15 / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Nucleolar GTP-binding protein 1 / Ribosome biogenesis protein RLP24 / Regulator of ribosome biosynthesis / Ribosome biogenesis protein NOP53 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMilkereit, P. / Poell, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 960 Germany
CitationJournal: PLoS One / Year: 2021
Title: Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors.
Authors: Gisela Pöll / Michael Pilsl / Joachim Griesenbeck / Herbert Tschochner / Philipp Milkereit /
Abstract: In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with ...In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits.
History
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 10, 2021Group: Atomic model / Data collection
Category: atom_site / em_admin ...atom_site / em_admin / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _em_admin.last_update / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 2.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2Jul 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
1: 25S rRNA
2: 5.8S rRNA
3: 5S rRNA
5: rRNA-processing protein CGR1
6: ITS2
A: 60S ribosomal protein L2-A
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4-A
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6-A
F: 60S ribosomal protein L7-A
G: 60S ribosomal protein L8-A
H: 60S ribosomal protein L9-A
J: 60S ribosomal protein L11-A
K: Proteasome-interacting protein CIC1
L: 60S ribosomal protein L13-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L15-A
O: 60S ribosomal protein L16-A
P: 60S ribosomal protein L17-A
Q: 60S ribosomal protein L18-A
R: 60S ribosomal protein L19-A
S: 60S ribosomal protein L20-A
T: 60S ribosomal protein L21-A
U: 60S ribosomal protein L22-A
V: 60S ribosomal protein L23-A
W: Ribosome assembly factor MRT4
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28
b: Nucleolar GTP-binding protein 1
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31-A
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
g: 60S ribosomal protein L34-A
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
l: 60S ribosomal protein L39
m: Nucleolar GTP-binding protein 2
n: Pescadillo homolog
o: Ribosome biogenesis protein 15
p: 60S ribosomal protein L43-A
q: Ribosome biogenesis protein NOP53
r: Ribosome biogenesis protein NSA2
s: Nuclear GTP-binding protein NUG1
t: Ribosome biogenesis protein RLP7
u: Ribosome biogenesis protein RLP24
v: Ribosome biogenesis protein RPF2
w: Regulator of ribosome biosynthesis
x: Ribosome assembly protein 4
y: Eukaryotic translation initiation factor 6
z: UPF0642 protein YBL028C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,594,68161
Polymers2,594,43656
Non-polymers2455
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area450600 Å2
ΔGint-3281 kcal/mol
Surface area761470 Å2
MethodPISA

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Components

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RNA chain , 4 types, 4 molecules 1236

#1: RNA chain 25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 834774822
#2: RNA chain 5.8S rRNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 940534893
#3: RNA chain 5S rRNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 834774822
#5: RNA chain ITS2


Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)

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Protein , 7 types, 7 molecules 5Knswyz

#4: Protein rRNA-processing protein CGR1 / Coiled-coil growth-regulated protein 1


Mass: 14460.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53188
#15: Protein Proteasome-interacting protein CIC1 / Core interacting component 1


Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38779
#44: Protein Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53261
#49: Protein Nuclear GTP-binding protein NUG1 / Nuclear GTPase 1


Mass: 57798.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40010
#53: Protein Regulator of ribosome biosynthesis


Mass: 23001.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08746
#55: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12522
#56: Protein UPF0642 protein YBL028C


Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38202

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60S ribosomal protein ... , 35 types, 35 molecules ABCDEFGHJLMNOPQRSTUVXYZacdefgh...

#6: Protein 60S ribosomal protein L2-A / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#7: Protein 60S ribosomal protein L3 / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14126
#8: Protein 60S ribosomal protein L4-A / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10664
#9: Protein 60S ribosomal protein L5 / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26321
#10: Protein 60S ribosomal protein L6-A / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02326
#11: Protein 60S ribosomal protein L7-A / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05737
#12: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P17076
#13: Protein 60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05738
#14: Protein 60S ribosomal protein L11-A / L16 / Large ribosomal subunit protein uL5-A / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W9
#16: Protein 60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#17: Protein 60S ribosomal protein L14-A / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36105
#18: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05748
#19: Protein 60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26784
#20: Protein 60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05740
#21: Protein 60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#22: Protein 60S ribosomal protein L19-A / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#23: Protein 60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#24: Protein 60S ribosomal protein L21-A / Large ribosomal subunit protein eL21-A


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02753
#25: Protein 60S ribosomal protein L22-A / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05749
#26: Protein 60S ribosomal protein L23-A / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#28: Protein 60S ribosomal protein L25 / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04456
#29: Protein 60S ribosomal protein L26-A / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05743
#30: Protein 60S ribosomal protein L27-A / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#31: Protein 60S ribosomal protein L28 / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02406
#33: Protein 60S ribosomal protein L30 / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14120
#34: Protein 60S ribosomal protein L31-A / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H8
#35: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38061
#36: Protein 60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05744
#37: Protein 60S ribosomal protein L34-A / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P87262
#38: Protein 60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#39: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05745
#40: Protein 60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49166
#41: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49167
#42: Protein 60S ribosomal protein L39 / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04650
#46: Protein 60S ribosomal protein L43-A / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX25

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Ribosome assembly ... , 2 types, 2 molecules Wx

#27: Protein Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33201
#54: Protein Ribosome assembly protein 4 / Notchless protein homolog 1 / Ribosome biogenesis factor RSA4


Mass: 57106.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25382

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Nucleolar GTP-binding protein ... , 2 types, 2 molecules bm

#32: Protein Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02892
#43: Protein Nucleolar GTP-binding protein 2


Mass: 55585.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53742

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Ribosome biogenesis protein ... , 6 types, 6 molecules oqrtuv

#45: Protein Ribosome biogenesis protein 15 / Nucleolar protein 15


Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53927
#47: Protein Ribosome biogenesis protein NOP53 / Nucleolar protein 53


Mass: 52667.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12080
#48: Protein Ribosome biogenesis protein NSA2 / NOP7-associated protein 2


Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40078
#50: Protein Ribosome biogenesis protein RLP7 / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40693
#51: Protein Ribosome biogenesis protein RLP24 / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07915
#52: Protein Ribosome biogenesis protein RPF2


Mass: 39665.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36160

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Non-polymers , 2 types, 5 molecules

#57: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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: Nog1-TAP associated immature ribosomal particles. / Type: RIBOSOME
Details: Sample obtained from cellular extracts via affinity purification.
Entity ID: #1-#56 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
1200 mMpotassium chloride1
25 mMmagnesium acetate1
320 mMTris pH81
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 5.16 sec. / Electron dose: 84.67 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraX 1.0model fitting
9ISOLDE1.1model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34162 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 3JCT

3jct


Accession code: 3JCT / Source name: PDB / Type: experimental model

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