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- PDB-7wts: Cryo-EM structure of a human pre-40S ribosomal subunit - State UTP14 -

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Entry
Database: PDB / ID: 7wts
TitleCryo-EM structure of a human pre-40S ribosomal subunit - State UTP14
Components
  • (40S ribosomal protein ...) x 14
  • 18S rRNA18S ribosomal RNA
  • Multifunctional methyltransferase subunit TRM112-like protein
  • Pre-rRNA-processing protein TSR1 homolog
  • Probable 18S rRNA (guanine-N(7))-methyltransferase
  • Probable dimethyladenosine transferase
  • RNA-binding protein PNO1
  • RRP12-like protein
  • Ribosome biogenesis protein SLX9 homolog
  • U3 small nucleolar RNA-associated protein 14 homolog A
KeywordsRIBOSOME / ribosome biogenesis / 40S ribosome
Function / homology
Function and homology information


18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / peptidyl-glutamine methylation / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Methylation ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / peptidyl-glutamine methylation / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / negative regulation of RNA splicing / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / rRNA methylation / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / U3 snoRNA binding / ubiquitin ligase inhibitor activity / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / 90S preribosome / mTORC1-mediated signalling / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / rough endoplasmic reticulum / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cell cycle / stress granule assembly / translation initiation factor binding / maturation of SSU-rRNA / Mitotic Prometaphase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / EML4 and NUDC in mitotic spindle formation / negative regulation of ubiquitin-dependent protein catabolic process / translational initiation / transcription initiation-coupled chromatin remodeling / Resolution of Sister Chromatid Cohesion / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / cytosolic ribosome / erythrocyte differentiation / positive regulation of translation / innate immune response in mucosa / mRNA 3'-UTR binding / neural tube closure / methyltransferase activity / RHO GTPases Activate Formins / maintenance of translational fidelity / response to virus / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / cytoplasmic ribonucleoprotein granule / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / Regulation of expression of SLITs and ROBOs / Separation of Sister Chromatids / cytosolic small ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / cell body / cytoplasmic translation / small ribosomal subunit / chromatin organization / antibacterial humoral response / SARS-CoV-2 modulates host translation machinery / nuclear membrane / postsynaptic density / cell differentiation / rRNA binding / protein stabilization / ribosome / structural constituent of ribosome / defense response to Gram-positive bacterium / ribonucleoprotein complex / translation / positive regulation of apoptotic process / protein heterodimerization activity / focal adhesion
Similarity search - Function
Ribosome biogenesis protein Slx9-like / Ribosome biogenesis protein SLX9 / Uncharacterised domain NUC173 / Ribosomal RNA-processing protein 12, HEAT repeats / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein ...Ribosome biogenesis protein Slx9-like / Ribosome biogenesis protein SLX9 / Uncharacterised domain NUC173 / Ribosomal RNA-processing protein 12, HEAT repeats / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase type 11 / Small-subunit processome, Utp14 / Utp14 protein / Methyltransferase domain / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / Ubiquitin-like protein FUBI / K Homology domain, type 1 superfamily / : / Ribosomal protein S30 / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S6/S6e/A/B/2, conserved site / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / K Homology domain / K homology RNA-binding domain / : / Armadillo-like helical / Ribosomal protein S17, conserved site / Ubiquitin family / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / Ubiquitin homologues
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Probable 18S rRNA (guanine-N(7))-methyltransferase / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Probable 18S rRNA (guanine-N(7))-methyltransferase / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Pre-rRNA-processing protein TSR1 homolog / RRP12-like protein / U3 small nucleolar RNA-associated protein 14 homolog A / RNA-binding protein PNO1 / Ribosome biogenesis protein SLX9 homolog / Multifunctional methyltransferase subunit TRM112-like protein / Probable dimethyladenosine transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCheng, J. / Lau, B. / Thoms, M. / Ameismeier, M. / Berninghausen, O. / Hurt, E. / Beckmann, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2022
Title: The nucleoplasmic phase of pre-40S formation prior to nuclear export.
Authors: Jingdong Cheng / Benjamin Lau / Matthias Thoms / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann /
Abstract: Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural ...Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.
History
DepositionFeb 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: 18S rRNA
b: 40S ribosomal protein S27
B: 40S ribosomal protein S3a
E: 40S ribosomal protein S4, X isoform
e: 40S ribosomal protein S30
H: 40S ribosomal protein S7
G: 40S ribosomal protein S6
Y: 40S ribosomal protein S24
x: RNA-binding protein PNO1
X: 40S ribosomal protein S23
W: 40S ribosomal protein S15a
u: Pre-rRNA-processing protein TSR1 homolog
O: 40S ribosomal protein S14
N: 40S ribosomal protein S13
L: 40S ribosomal protein S11
J: 40S ribosomal protein S9
I: 40S ribosomal protein S8
r: Multifunctional methyltransferase subunit TRM112-like protein
q: Probable 18S rRNA (guanine-N(7))-methyltransferase
K: RRP12-like protein
z: Ribosome biogenesis protein SLX9 homolog
5: U3 small nucleolar RNA-associated protein 14 homolog A
3: Probable dimethyladenosine transferase


Theoretical massNumber of molelcules
Total (without water)1,334,84323
Polymers1,334,84323
Non-polymers00
Water0
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 , 1 types, 1 molecules 2

#1: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 604102.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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40S ribosomal protein ... , 14 types, 14 molecules bBEeHGYXWONLJI

#2: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#3: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#4: Protein 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#5: Protein 40S ribosomal protein S30 / / Small ribosomal subunit protein eS30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#6: Protein 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#7: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#8: Protein 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#10: Protein 40S ribosomal protein S23 / / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#11: Protein 40S ribosomal protein S15a / / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#13: Protein 40S ribosomal protein S14 / / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#14: Protein 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#15: Protein 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#16: Protein 40S ribosomal protein S9 / / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#17: Protein 40S ribosomal protein S8 / / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241

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Protein , 8 types, 8 molecules xurqKz53

#9: Protein RNA-binding protein PNO1 / Partner of NOB1


Mass: 27970.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX1
#12: Protein Pre-rRNA-processing protein TSR1 homolog


Mass: 91951.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q2NL82
#18: Protein Multifunctional methyltransferase subunit TRM112-like protein


Mass: 14215.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UI30
#19: Protein Probable 18S rRNA (guanine-N(7))-methyltransferase / Bud site selection protein 23 homolog / Metastasis-related methyltransferase 1 / Williams-Beuren ...Bud site selection protein 23 homolog / Metastasis-related methyltransferase 1 / Williams-Beuren syndrome chromosomal region 22 protein / rRNA methyltransferase and ribosome maturation factor


Mass: 31925.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O43709, Transferases; Transferring one-carbon groups; Methyltransferases
#20: Protein RRP12-like protein


Mass: 143916.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5JTH9
#21: Protein Ribosome biogenesis protein SLX9 homolog /


Mass: 25503.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NSI2
#22: Protein U3 small nucleolar RNA-associated protein 14 homolog A / Antigen NY-CO-16 / Serologically defined colon cancer antigen 16


Mass: 88129.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BVJ6
#23: Protein Probable dimethyladenosine transferase / DIM1 dimethyladenosine transferase 1 homolog / DIM1 dimethyladenosine transferase 1-like / Probable ...DIM1 dimethyladenosine transferase 1 homolog / DIM1 dimethyladenosine transferase 1-like / Probable 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / Probable 18S rRNA dimethylase / Probable S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 35292.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UNQ2, 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase

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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-40S ribosomal subunit / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
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 FIELDBright-field microscopy / 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 correctionDetails: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8843 / Symmetry type: POINT

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