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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 / cytosol / cytoplasm
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 / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e signature. / 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 L35Ae signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / 60S ribosomal protein L6E / 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 L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae / Ribosomal protein L32e signature. / Ribosomal protein L35A superfamily / 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 L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L30, ferredoxin-like fold domain 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: To Be Published
Title: A comprehensive view on r- protein binding and rRNA domain structuring during early ribosome formation
Authors: Gerhalter, M. / Prattes, M. / Grundmann, L. / Grishkovskaya, I. / Semarari, E.F. / Zisser, G. / Harald, K. / Merl-Pharm, J. / Hauck, S.M. / Haselbach, D. / Bergler, H.
History
DepositionMar 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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