- EMDB-25441: Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Proc... -
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Basic information
Entry
Database: EMDB / ID: EMD-25441
Title
Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells
Map data
Composite map
Sample
Complex: Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells
Protein or peptide: x 63 types
RNA: x 3 types
Keywords
Bfr2 / Lcp5 / Small subunit processome / RIBOSOMAL PROTEIN / RIBOSOME
Function / homology
Function and homology information
rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / box H/ACA snoRNA binding / tRNA N4-acetyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA acetylation / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation ...rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / box H/ACA snoRNA binding / tRNA N4-acetyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA acetylation / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / t-UTP complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / box C/D sno(s)RNA binding / septum digestion after cytokinesis / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA 3'-end processing / rDNA heterochromatin / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / box C/D methylation guide snoRNP complex / single-stranded telomeric DNA binding / tRNA export from nucleus / rRNA primary transcript binding / rRNA base methylation / sno(s)RNA-containing ribonucleoprotein complex / 90S preribosome assembly / O-methyltransferase activity / small nuclear ribonucleoprotein complex / rRNA methylation / histone H2A Q104 methyltransferase activity / mTORC1-mediated signalling / Protein hydroxylation / mRNA modification / U3 snoRNA binding / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / poly(A)+ mRNA export from nucleus / Translation initiation complex formation / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / snoRNA binding / establishment of cell polarity / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / 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 / proteasome assembly / 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) / RNA processing / regulation of translational fidelity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / vesicle-mediated transport / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / enzyme activator activity / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / rRNA processing / unfolded protein binding / protein transport / ribosome biogenesis / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / mitochondrion / RNA binding Similarity search - Function
Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Protein AATF/Bfr2 / : / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / NUC153 / Nucleolar protein 10/Enp2 ...Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Protein AATF/Bfr2 / : / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / NUC153 / Nucleolar protein 10/Enp2 / NUC153 domain / U3 small nucleolar RNA-associated protein 8 / : / Utp8, N-terminal beta propeller / Utp8, C-terminal / rRNA biogenesis protein Rrp5 / : / : / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 snoRNA associated / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 20, C-terminal / : / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 snoRNA associated / U3 small nucleolar RNA-associated protein 20 domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / NOL6/Upt22 / Small-subunit processome, Utp11 / Sof1-like protein / BING4, C-terminal domain / Fcf2 pre-rRNA processing, C-terminal / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / rRNA-processing protein Fcf1, PIN domain / Fcf2/DNTTIP2 / WD repeat-containing protein WDR46/Utp7 / : / : / Nrap protein domain 1 / Utp11 protein / Sof1-like domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / BING4CT (NUC141) domain / rRNA-processing protein Fcf1/Utp23 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / Fcf1 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Sas10/Utp3/C1D / Small-subunit processome, Utp21 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2 / Sas10/Utp3/C1D family / Mpp10 protein / Utp21 specific WD40 associated putative domain / Ribosomal RNA-processing protein Rrp9-like / RNA 3'-terminal phosphate cyclase / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily Similarity search - Domain/homology
Ribonucloprotein / RRP9 isoform 1 / Nucleolar protein 58 / U3 small nucleolar RNA-associated protein 11 / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS4A ...Ribonucloprotein / RRP9 isoform 1 / Nucleolar protein 58 / U3 small nucleolar RNA-associated protein 11 / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS9A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / Periodic tryptophan protein 2 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein SOF1 / U3 small nucleolar RNA-associated protein 20 / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / Small ribosomal subunit protein uS11B / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar ribonucleoprotein protein LCP5 / U3 small nucleolar RNA-associated protein 18 / Regulator of rDNA transcription protein 14 / Protein FAF1 / U3 small nucleolar RNA-associated protein MPP10 / Ribosome biogenesis protein ENP2 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 8 / RNA cytidine acetyltransferase / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 15 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Nucleolar complex protein 4 / Protein BFR2 / RNA 3'-terminal phosphate cyclase-like protein / U3 small nucleolar RNA-associated protein 16 / rRNA-processing protein FCF2 / Small ribosomal subunit protein eS28A / Pre-rRNA-processing protein PNO1 Similarity search - Component
Biological species
Saccharomyces cerevisiae (brewer's yeast)
Method
single particle reconstruction / cryo EM / Resolution: 3.99 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01 GM124622
United States
Citation
Journal: Commun Biol / Year: 2022 Title: Artificial intelligence-assisted cryoEM structure of Bfr2-Lcp5 complex observed in the yeast small subunit processome. Authors: Yu Zhao / Jay Rai / Chong Xu / Huan He / Hong Li / Abstract: Eukaryotic ribosome is maturated through an elaborate process that includes modification, processing and folding of pre-ribosomal RNA (pre-rRNAs) by a series of ribosome assembly intermediates. More ...Eukaryotic ribosome is maturated through an elaborate process that includes modification, processing and folding of pre-ribosomal RNA (pre-rRNAs) by a series of ribosome assembly intermediates. More than 70 factors participate in the dynamic assembly and disassembly of the small subunit processome (90S) inside nucleolus, leading to the early maturation of small subunit. The 5' domain of the 18S rRNA is the last to be incorporated into the stable 90S prior to the cleavage of pre-rRNA at the A1 site. This step is facilitated by the Kre33-Enp2-Bfr2-Lcp5 protein module with the participation of the DEAD-box protein Dbp4. Though structures of Kre33 and Enp2 have been modeled in previously observed 90S structures, that of Bfr2-Lcp5 complex remains unavailable. Here, we report an AlphaFold-assisted structure determination of the Bfr2-Lcp5 complex captured in a 3.99 Å - 7.24 Å cryoEM structure of 90S isolated from yeast cells depleted of Pih1, a chaperone protein of the 90S core assembly. The structure model is consistent with the protein-protein interaction results and the secondary structures of recombinant Bfr2 and Bfr2-Lcp5 complex obtained by Circular Dichroism. The Bfr2-Lcp5 complex interaction mimics that of exosome factors Rrp6-Rrp47 and acts to regulate 90S transitions.
UniProtKB: U3 small nucleolar RNA-associated protein 20
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Macromolecule #62: RNA cytidine acetyltransferase
Macromolecule
Name: RNA cytidine acetyltransferase / type: protein_or_peptide / ID: 62 / Number of copies: 2 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
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