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- PDB-9g25: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 -

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Basic information

Entry
Database: PDB / ID: 9g25
TitlesnR30 snoRNP - State 1 - Utp23-Krr1-deltaC3
Components
  • (40S ribosomal protein ...) x 2
  • (H/ACA ribonucleoprotein complex subunit ...) x 4
  • KRR1 small subunit processome component
  • Protein KRI1
  • RDN18-1
  • rRNA-processing protein UTP23
  • snR30
KeywordsRIBOSOME / 90S / pre-ribosome / snoRNA / snR30 / snoRNP / ribosome biogenesis / H/ACA / 18S rRNA
Function / homology
Function and homology information


snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / Isomerases; Intramolecular transferases; Transferring other groups / snRNA pseudouridine synthesis / box H/ACA snoRNA binding ...snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / Isomerases; Intramolecular transferases; Transferring other groups / snRNA pseudouridine synthesis / box H/ACA snoRNA binding / mRNA pseudouridine synthesis / pseudouridine synthase activity / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / sno(s)RNA-containing ribonucleoprotein complex / telomerase RNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / snoRNA binding / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / 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 / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / chromosome, centromeric region / 90S preribosome / 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 SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / microtubule / cytoplasmic translation / structural constituent of ribosome / translation / cell division / mRNA binding / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
KRR1 interacting protein 1 / Kri1-like, C-terminal / KRI1-like family / KRI1-like family C-terminal / UTP23 sensor motif / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like ...KRR1 interacting protein 1 / Kri1-like, C-terminal / KRI1-like family / KRI1-like family C-terminal / UTP23 sensor motif / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / Uncharacterised domain CHP00451 / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / PUA domain / rRNA-processing protein Fcf1/Utp23 / Fcf1 / Krr1, KH1 domain / Krr1 KH1 domain / Pseudouridine synthase, catalytic domain superfamily / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / PUA domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / K Homology domain, type 1 superfamily / PIN-like domain superfamily / PUA-like superfamily / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / K Homology domain / K homology RNA-binding domain / Ribosomal protein S15 signature. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / Ribosomal protein S11 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / KRR1 small subunit processome component / H/ACA ribonucleoprotein complex subunit GAR1 / H/ACA ribonucleoprotein complex subunit NHP2 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / KRR1 small subunit processome component / H/ACA ribonucleoprotein complex subunit GAR1 / H/ACA ribonucleoprotein complex subunit NHP2 / H/ACA ribonucleoprotein complex subunit CBF5 / Protein KRI1 / rRNA-processing protein UTP23 / H/ACA ribonucleoprotein complex subunit NOP10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsThoms, M. / Berninghausen, O. / Beckmann, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Citation
Journal: Nat Commun / Year: 2025
Title: H/ACA snR30 snoRNP guides independent 18S rRNA subdomain formation.
Authors: Paulina Fischer / Matthias Thoms / Benjamin Lau / Timo Denk / Maria Kuvshinova / Otto Berninghausen / Dirk Flemming / Ed Hurt / Roland Beckmann /
Abstract: Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, ...Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, composed of pre-18S rRNA, ribosomal S-proteins, U3 snoRNA, and ~70 assembly factors. However, how numerous snoRNAs control pre-rRNA modification and folding during early maturation events remains unclear. We identify snR30 (human U17), the only essential H/ACA snoRNA in yeast, which binds with Cbf5-Gar1-Nop10-Nhp2 to a pre-18S rRNA subdomain containing platform helices and ES6 of the 40S central domain. Integration into the 90S is blocked by RNA hybridization with snR30. The snoRNP complex coordinates the recruitment of early assembly factors Krr1-Utp23-Kri1 and ribosomal proteins uS11-uS15, enabling isolated subdomain assembly. Krr1-dependent release of snR30 culminates in integration of the platform into the 90S. Our study reveals the essential role of snR30 in chaperoning central domain formation as a discrete assembly unit externalized from the pre-ribosomal core.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Adams, P.D.
History
DepositionJul 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: RDN18-1
4: snR30
A: H/ACA ribonucleoprotein complex subunit CBF5
B: H/ACA ribonucleoprotein complex subunit NOP10
C: H/ACA ribonucleoprotein complex subunit GAR1
D: H/ACA ribonucleoprotein complex subunit NHP2
E: H/ACA ribonucleoprotein complex subunit CBF5
F: H/ACA ribonucleoprotein complex subunit NOP10
G: H/ACA ribonucleoprotein complex subunit NHP2
H: KRR1 small subunit processome component
I: Protein KRI1
J: 40S ribosomal protein S13
K: rRNA-processing protein UTP23
L: 40S ribosomal protein S14-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,120,47715
Polymers1,120,41214
Non-polymers651
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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RNA chain , 2 types, 2 molecules 34

#1: RNA chain RDN18-1


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 874346701
#2: RNA chain snR30


Mass: 195416.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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H/ACA ribonucleoprotein complex subunit ... , 4 types, 7 molecules AEBFCDG

#3: Protein H/ACA ribonucleoprotein complex subunit CBF5 / Centromere-binding factor 5 / Centromere/microtubule-binding protein CBF5 / H/ACA snoRNP protein ...Centromere-binding factor 5 / Centromere/microtubule-binding protein CBF5 / H/ACA snoRNP protein CBF5 / Small nucleolar RNP protein CBF5 / p64'


Mass: 54804.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P33322, Isomerases; Intramolecular transferases; Transferring other groups
#4: Protein H/ACA ribonucleoprotein complex subunit NOP10 / Nucleolar protein 10 / Nucleolar protein family A member 3 / snoRNP protein NOP10


Mass: 6649.745 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q6Q547
#5: Protein H/ACA ribonucleoprotein complex subunit GAR1 / Glycine/arginine-rich protein 1 / snoRNP protein GAR1


Mass: 21520.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P28007
#6: Protein H/ACA ribonucleoprotein complex subunit NHP2 / H/ACA snoRNP protein NHP2 / High mobility group-like nuclear protein 2


Mass: 17158.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32495

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Protein , 3 types, 3 molecules HIK

#7: Protein KRR1 small subunit processome component / KRR-R motif-containing protein 1 / Ribosomal RNA assembly protein KRR1


Mass: 37226.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25586
#8: Protein Protein KRI1 / KRR1-interacting protein 1


Mass: 68778.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P42846
#10: Protein rRNA-processing protein UTP23 / U three protein 23 / U3 small nucleolar RNA-associated protein 23 / U3 snoRNA-associated protein 23


Mass: 28859.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12339

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40S ribosomal protein ... , 2 types, 2 molecules JL

#9: Protein 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#11: Protein 40S ribosomal protein S14-A / RP59A / Small ribosomal subunit protein uS11-A


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367

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Non-polymers , 1 types, 1 molecules

#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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: Utp23-FTpA, Krr1-deltaC3 / Type: RIBOSOME / Entity ID: #1-#11 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
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: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 46.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171224
Details: Note: This is a composite map. The resolution given refers to the consensus refinement.
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003425214
ELECTRON MICROSCOPYf_angle_d0.672135847
ELECTRON MICROSCOPYf_chiral_restr0.044379
ELECTRON MICROSCOPYf_plane_restr0.00593212
ELECTRON MICROSCOPYf_dihedral_angle_d12.59216656

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