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Yorodumi- EMDB-25441: Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Proc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25441 | |||||||||
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Title | Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells | |||||||||
Map data | Composite map | |||||||||
Sample |
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Keywords | Bfr2 / Lcp5 / Small subunit processome / RIBOSOMAL PROTEIN / RIBOSOME | |||||||||
Function / homology | Function and homology information rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / mRNA modification / Noc4p-Nop14p complex / tRNA acetylation / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process ...rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / mRNA modification / Noc4p-Nop14p complex / tRNA acetylation / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / histone H2AQ104 methyltransferase activity / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / regulation of transcription by RNA polymerase I / 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) / rDNA heterochromatin / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA base methylation / single-stranded telomeric DNA binding / rRNA primary transcript binding / 90S preribosome assembly / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / O-methyltransferase activity / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / poly(U) RNA binding / : / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / snoRNA binding / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / nucleolar large rRNA transcription by RNA polymerase I / 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 / enzyme activator activity / proteasome assembly / 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) / regulation of translational fidelity / RNA processing / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / RNA endonuclease activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / vesicle-mediated transport / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / small-subunit processome / maintenance of translational fidelity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / unfolded protein binding / protein transport / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.99 Å | |||||||||
Authors | Rai J / Zhao Y / Li H | |||||||||
Funding support | United States, 1 items
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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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25441.map.gz | 279.5 MB | EMDB map data format | |
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Header (meta data) | emd-25441-v30.xml emd-25441.xml | 100.6 KB 100.6 KB | Display Display | EMDB header |
Images | emd_25441.png | 99.5 KB | ||
Others | emd_25441_additional_1.map.gz emd_25441_additional_2.map.gz emd_25441_additional_3.map.gz | 288.4 MB 286.7 MB 282.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25441 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25441 | HTTPS FTP |
-Related structure data
Related structure data | 7sukMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25441.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.074 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Core region (3.99 Angstorm) from 199,534 particles.
File | emd_25441_additional_1.map | ||||||||||||
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Annotation | Core region (3.99 Angstorm) from 199,534 particles. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Central Domain (7.24 Angstorm) from 199,534 particles.
File | emd_25441_additional_2.map | ||||||||||||
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Annotation | Central Domain (7.24 Angstorm) from 199,534 particles. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Head domain (5.04 Angstorm) from 84,570 particles.
File | emd_25441_additional_3.map | ||||||||||||
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Annotation | Head domain (5.04 Angstorm) from 84,570 particles. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Proc...
+Supramolecule #1: Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Proc...
+Macromolecule #1: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #2: Nucleolar protein 56
+Macromolecule #3: Something about silencing protein 10
+Macromolecule #6: 40S ribosomal protein S18-A
+Macromolecule #7: 40S ribosomal protein S4-A
+Macromolecule #8: 40S ribosomal protein S5
+Macromolecule #9: 40S ribosomal protein S7-A
+Macromolecule #10: 40S ribosomal protein S8-A
+Macromolecule #11: 40S ribosomal protein S9-A
+Macromolecule #12: 40S ribosomal protein S16-A
+Macromolecule #13: 40S ribosomal protein S11-A
+Macromolecule #14: 40S ribosomal protein S22-A
+Macromolecule #15: 40S ribosomal protein S24-A
+Macromolecule #16: 40S ribosomal protein S28-A
+Macromolecule #17: NET1-associated nuclear protein 1
+Macromolecule #18: U3 small nucleolar RNA-associated protein 15
+Macromolecule #19: U3 small nucleolar RNA-associated protein 9
+Macromolecule #20: U3 small nucleolar RNA-associated protein 5
+Macromolecule #21: U3 small nucleolar RNA-associated protein 10
+Macromolecule #22: U3 small nucleolar RNA-associated protein 4
+Macromolecule #23: Periodic tryptophan protein 2
+Macromolecule #24: U3 small nucleolar RNA-associated protein 6
+Macromolecule #25: U3 small nucleolar RNA-associated protein 12
+Macromolecule #26: U3 small nucleolar RNA-associated protein 18
+Macromolecule #27: U3 small nucleolar RNA-associated protein 21
+Macromolecule #28: Protein SOF1
+Macromolecule #29: Ribosome biogenesis protein ENP2
+Macromolecule #30: U3 small nucleolar RNA-associated protein 7
+Macromolecule #31: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #32: 40S ribosomal protein S14-B
+Macromolecule #33: KRR1 small subunit processome component
+Macromolecule #34: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #35: Ribonucloprotein
+Macromolecule #36: RRP9 isoform 1
+Macromolecule #37: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #38: Ribosome biogenesis protein BMS1
+Macromolecule #39: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #40: rRNA-processing protein FCF1
+Macromolecule #41: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #42: Ribosome biogenesis protein UTP30
+Macromolecule #43: Pre-rRNA-processing protein PNO1
+Macromolecule #44: rRNA-processing protein FCF2
+Macromolecule #45: 40S ribosomal protein S23-A
+Macromolecule #46: U3 small nucleolar RNA-associated protein 14
+Macromolecule #47: Nucleolar complex protein 14
+Macromolecule #48: U3 small nucleolar RNA-associated protein 11
+Macromolecule #49: Essential nuclear protein 1
+Macromolecule #50: rRNA biogenesis protein RRP5
+Macromolecule #51: U3 small nucleolar RNA-associated protein 22
+Macromolecule #52: Ribosomal RNA-processing protein 7
+Macromolecule #54: Nucleolar complex protein 4
+Macromolecule #55: U3 small nucleolar RNA-associated protein 8
+Macromolecule #56: Bud site selection protein 21
+Macromolecule #57: U3 small nucleolar RNA-associated protein 13
+Macromolecule #58: Protein FAF1
+Macromolecule #59: Nucleolar protein 58
+Macromolecule #60: Regulator of rDNA transcription protein 14
+Macromolecule #61: U3 small nucleolar RNA-associated protein 20
+Macromolecule #62: RNA cytidine acetyltransferase
+Macromolecule #63: 40S ribosomal protein S6-A
+Macromolecule #64: 40S ribosomal protein S13
+Macromolecule #65: Protein BFR2
+Macromolecule #66: U3 small nucleolar ribonucleoprotein protein LCP5
+Macromolecule #4: 5' ETS
+Macromolecule #5: U3 snoRNA
+Macromolecule #53: 18S pre-rRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.074 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199534 |