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- PDB-9qjc: Yeast pre-60S Domain II intermediate -

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Basic information

Entry
Database: PDB / ID: 9qjc
TitleYeast pre-60S Domain II intermediate
Components
  • (60S ribosomal protein ...) x 9
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • Nucleolar complex protein 2
  • Nucleolar protein 4
  • Protein MAK16
  • Ribosomal RNA-processing protein 1
  • Ribosome biogenesis protein MAK21
KeywordsRIBOSOME / preLSU / preribosome / complex / Noc2-TAP particle
Function / homology
Function and homology information


Noc1p-Noc2p complex / Noc2p-Noc3p complex / 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 / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...Noc1p-Noc2p complex / Noc2p-Noc3p complex / 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 / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / rRNA processing / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / structural constituent of ribosome / ribosome / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nop4, RNA recognition motif 1 / Nop4, RNA recognition motif 2 / Nop4, RNA recognition motif 3 / Nop4, RNA recognition motif 4 / CEBPZ/Mak21-like / : / Nucleolar complex protein 2 / Noc2p family / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 ...Nop4, RNA recognition motif 1 / Nop4, RNA recognition motif 2 / Nop4, RNA recognition motif 3 / Nop4, RNA recognition motif 4 / CEBPZ/Mak21-like / : / Nucleolar complex protein 2 / Noc2p family / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / CCAAT-binding factor / CBF/Mak21 family / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein L6e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / 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 L35Ae, conserved site / 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 signature. / Ribosomal Protein L6, KOW domain / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L6E / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L18e / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L14 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal protein L32 / Ribosomal_L32e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Armadillo-type fold / KOW motif / KOW / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL18A ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL4A / Protein MAK16 / Large ribosomal subunit protein uL13A / Ribosomal RNA-processing protein 1 / Large ribosomal subunit protein eL14A / Nucleolar protein 4 / Large ribosomal subunit protein eL32 / Nucleolar complex protein 2 / Large ribosomal subunit protein eL6A / Ribosome biogenesis protein MAK21
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGrundmann, L. / Gerhalter, M. / Prattes, M. / Grishkovskaya, I. / Kotisch, H. / Haselbach, D. / Bergler, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundPAT1908524 Austria
CitationJournal: Nucleic Acids Res / Year: 2026
Title: A comprehensive view on r-protein binding and rRNA domain structuring during early eukaryotic ribosome formation.
Authors: Magdalena Gerhalter / Michael Prattes / Lorenz Emanuel Grundmann / Irina Grishkovskaya / Enrico F Semeraro / Gertrude Zisser / Harald Kotisch / Juliane Merl-Pham / Stefanie M Hauck / David ...Authors: Magdalena Gerhalter / Michael Prattes / Lorenz Emanuel Grundmann / Irina Grishkovskaya / Enrico F Semeraro / Gertrude Zisser / Harald Kotisch / Juliane Merl-Pham / Stefanie M Hauck / David Haselbach / Helmut Bergler /
Abstract: Formation of the eukaryotic ribosomal subunits follows a strict regime to assemble ribosomal proteins (r-protein) with ribosomal RNAs (rRNA) while removing internal (ITS) and external (ETS) ...Formation of the eukaryotic ribosomal subunits follows a strict regime to assemble ribosomal proteins (r-protein) with ribosomal RNAs (rRNA) while removing internal (ITS) and external (ETS) transcribed rRNA spacers. During the early stages of large subunit (LSU) formation, ITS2, together with six assembly factors, forms the characteristic foot structure of early nuclear pre-LSU particles. Here, we address the function of this foot structure during the early stages of ribosome assembly. We present cryo-EM structures from wild-type cells and cells depleted for the foot structure factor Rlp7. We show that compaction of domain I of the 25S rRNA is strictly dependent on the presence of foot factors, while domain II folds independently. Furthermore, Rlp7-depletion accumulated small subunit (SSU) processome intermediates prior to A1 cleavage and compaction of the individual domains of the 18S rRNA, providing also novel insights into the SSU-assembly process. SILAC labeling and affinity purification of co-transcriptionally assembled pre-ribosomes enabled us to resolve the assembly line of most early binding r-proteins step by step. This showed that incorporation of r-proteins in eukaryotes neither follows the bacterial regime nor a strict linear co-transcriptional mode. Instead, seed r-proteins might structurally define the individual rRNA domains before their compaction and fixation in the context of early pre-ribosomes.
History
DepositionMar 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
5: Ribosome biogenesis protein MAK21
6: Nucleolar complex protein 2
C: 60S ribosomal protein L4-A
D: Protein MAK16
E: 60S ribosomal protein L6-A
F: 60S ribosomal protein L7-A
M: 60S ribosomal protein L14-A
O: 60S ribosomal protein L16-A
Q: 60S ribosomal protein L18-A
S: 60S ribosomal protein L20-A
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
z: Ribosomal RNA-processing protein 1
1: 25S ribosomal RNA
2: 5.8S ribosomal RNA
B: Nucleolar protein 4


Theoretical massNumber of molelcules
Total (without water)1,686,39816
Polymers1,686,39816
Non-polymers00
Water00
1


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

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Components

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Protein , 5 types, 5 molecules 56DzB

#1: Protein Ribosome biogenesis protein MAK21 / Maintenance of killer protein 21 / Nucleolar complex protein 1


Mass: 116832.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12176
#2: Protein Nucleolar complex protein 2


Mass: 81719.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NOC2, YOR206W, YOX001 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39744
#4: Protein Protein MAK16 / Maintenance of killer protein 16


Mass: 35754.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: MSDEIVWQVINQSFCSHRIKAPNGQNFCRNEYNVTGLCTRQSCPLANSKYATVKCDNGKLYLYMKTPERAHTPAKLWERIKLSKNYTKALQQIDEHLLHWSKFFRHKCKQRFTKLTQVMITERRLALREEERHYVGVAPKVKRREQNRERKALVAAKIEKAIEKELMDRLKSGAYGDKPLNVDEKVWKKIMGQMEEENSQDEEEDWDEEEESDDGEVEYVADDGEGEYVDVDDLEKWLADSDREASSASESESDSESESDSDSDEENKNSAKRRKKGTSAKTKRPKVEIEYEEEHEVQNAEQEVAQ
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAK16, YAL025C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10962
#13: Protein Ribosomal RNA-processing protein 1


Mass: 33250.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP1, YDR087C, D4478 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35178
#16: Protein Nucleolar protein 4 / Nucleolar protein NOP77


Mass: 77972.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NOP4, NOP77, YPL043W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P37838

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60S ribosomal protein ... , 9 types, 9 molecules CEFMOQSef

#3: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL4A, RPL2, RPL2A, YBR031W, YBR0315 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#5: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL6A, RPL17A, YL16A, YML073C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02326
#6: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL7A, RPL6A, RPL8A, YL8A, YGL076C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#7: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL14A, YKL006W, YKL153 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105
#8: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL16A, RPL13, RPL21A, YIL133C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#9: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL18A, RP28A, YOL120C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX49
#10: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX23
#11: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL32, YBL092W, YBL0838 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#12: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL33A, RPL37A, YPL143W, LPI4W, P2625 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05744

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RNA chain , 2 types, 2 molecules 12

#14: RNA chain 25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822
#15: RNA chain 5.8S ribosomal RNA


Mass: 51012.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1531397445

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Details

Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Yeast pre-60S Domain II / Type: RIBOSOME
Details: Noc2-TAP particle from yeast after Rpl7 depletion, where only Domain II adopts a structured conformation
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 4 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11250
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
5cryoSPARC3.0 - 4.6CTF correction
11cryoSPARC3.0 - 4.6final Euler assignment
13cryoSPARC3.0 - 4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54106 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 92.06 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003936628
ELECTRON MICROSCOPYf_angle_d0.549452088
ELECTRON MICROSCOPYf_chiral_restr0.03816324
ELECTRON MICROSCOPYf_plane_restr0.00434623
ELECTRON MICROSCOPYf_dihedral_angle_d19.495510928

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