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- PDB-7suk: Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Proc... -

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Entry
Database: PDB / ID: 7suk
TitleStructure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells
Components
  • (40S ribosomal protein ...) x 15
  • (Nucleolar complex protein ...) x 2
  • (Nucleolar protein ...Nucleolus) x 2
  • (Ribosome biogenesis protein ...) x 3
  • (U3 small nucleolar RNA-associated protein ...) x 17
  • (U3 small nucleolar ribonucleoprotein protein ...) x 3
  • (rRNA-processing protein ...) x 2
  • 18S pre-rRNA
  • 5' ETS
  • Bud site selection protein 21
  • Essential nuclear protein 1
  • KRR1 small subunit processome component
  • NET1-associated nuclear protein 1
  • Periodic tryptophan protein 2
  • Pre-rRNA-processing protein PNO1
  • Protein BFR2
  • Protein FAF1
  • Protein SOF1
  • RNA 3'-terminal phosphate cyclase-like protein
  • RNA cytidine acetyltransferase
  • RRP9 isoform 1
  • Regulator of rDNA transcription protein 14
  • Ribonucloprotein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Ribosomal RNA-processing protein 7
  • Something about silencing protein 10
  • U3 snoRNA
  • rRNA 2'-O-methyltransferase fibrillarin
  • rRNA biogenesis protein RRP5
KeywordsRIBOSOME / Bfr2 / Lcp5 / Small subunit processome / RIBOSOMAL PROTEIN
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
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 family / rRNA biogenesis protein Rrp5 / : / : / : / KRR1 small subunit processome component, second KH 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 / Ribosomal RNA assembly KRR1 / 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, C-terminal / rRNA-processing protein Fcf1, PIN domain / 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 / 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 / Ribosomal RNA-processing protein Rrp9-like / 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 biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase / 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 / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Nucleolar protein Nop56/Nop58 / CCAAT-binding factor / CBF/Mak21 family
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribonucloprotein / RRP9 isoform 1 / Nucleolar protein 58 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsRai, J. / Zhao, Y. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
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.
#1: 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
DepositionNov 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
NA: U3 small nucleolar RNA-associated protein MPP10
SA: Nucleolar protein 56
NB: Something about silencing protein 10
L0: 5' ETS
L2: U3 snoRNA
L3: 40S ribosomal protein S18-A
L4: 40S ribosomal protein S4-A
L5: 40S ribosomal protein S5
L7: 40S ribosomal protein S7-A
L8: 40S ribosomal protein S8-A
L9: 40S ribosomal protein S9-A
LC: 40S ribosomal protein S16-A
LD: 40S ribosomal protein S11-A
LE: 40S ribosomal protein S22-A
LF: 40S ribosomal protein S24-A
LG: 40S ribosomal protein S28-A
LH: NET1-associated nuclear protein 1
LJ: U3 small nucleolar RNA-associated protein 15
LK: U3 small nucleolar RNA-associated protein 9
LL: U3 small nucleolar RNA-associated protein 5
LM: U3 small nucleolar RNA-associated protein 10
LN: U3 small nucleolar RNA-associated protein 4
LO: Periodic tryptophan protein 2
LP: U3 small nucleolar RNA-associated protein 6
LQ: U3 small nucleolar RNA-associated protein 12
LS: U3 small nucleolar RNA-associated protein 18
LT: U3 small nucleolar RNA-associated protein 21
LU: Protein SOF1
LV: Ribosome biogenesis protein ENP2
LW: U3 small nucleolar RNA-associated protein 7
LZ: U3 small nucleolar ribonucleoprotein protein IMP3
NG: 40S ribosomal protein S14-B
NK: KRR1 small subunit processome component
SC: rRNA 2'-O-methyltransferase fibrillarin
SD: rRNA 2'-O-methyltransferase fibrillarin
SE: Ribonucloprotein
SF: Ribonucloprotein
SG: RRP9 isoform 1
SH: RNA 3'-terminal phosphate cyclase-like protein
SI: Ribosome biogenesis protein BMS1
SJ: Ribosomal RNA small subunit methyltransferase NEP1
SK: Ribosomal RNA small subunit methyltransferase NEP1
SL: rRNA-processing protein FCF1
SM: U3 small nucleolar ribonucleoprotein protein IMP4
SN: Ribosome biogenesis protein UTP30
SO: Pre-rRNA-processing protein PNO1
SQ: rRNA-processing protein FCF2
SR: 40S ribosomal protein S23-A
SS: U3 small nucleolar RNA-associated protein 14
ST: Nucleolar complex protein 14
SY: U3 small nucleolar RNA-associated protein 11
SZ: Essential nuclear protein 1
NJ: rRNA biogenesis protein RRP5
NH: U3 small nucleolar RNA-associated protein 22
NI: Ribosomal RNA-processing protein 7
8: 18S pre-rRNA
SU: Nucleolar complex protein 4
LI: U3 small nucleolar RNA-associated protein 8
ND: Bud site selection protein 21
LR: U3 small nucleolar RNA-associated protein 13
NE: Protein FAF1
SB: Nucleolar protein 58
SV: Regulator of rDNA transcription protein 14
SP: U3 small nucleolar RNA-associated protein 20
LY: RNA cytidine acetyltransferase
LX: RNA cytidine acetyltransferase
L6: 40S ribosomal protein S6-A
NF: 40S ribosomal protein S13
5: Protein BFR2
6: U3 small nucleolar ribonucleoprotein protein LCP5


Theoretical massNumber of molelcules
Total (without water)3,972,09870
Polymers3,972,09870
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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U3 small nucleolar RNA-associated protein ... , 17 types, 17 molecules NALJLKLLLMLNLPLQLSLTLWSSSYNHLILRSP

#1: Protein U3 small nucleolar RNA-associated protein MPP10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10


Mass: 28232.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47083
#18: Protein U3 small nucleolar RNA-associated protein 15 / U3 snoRNA-associated protein 15 / U three protein 15 / U3 protein 15 required for transcription / t-UTP15


Mass: 57765.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04305
#19: Protein U3 small nucleolar RNA-associated protein 9


Mass: 13282.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#20: Protein U3 small nucleolar RNA-associated protein 5 / U3 snoRNA-associated protein 5 / U three protein 5 / U3 protein 5 required for transcription / t-UTP5


Mass: 62177.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04177
#21: Protein U3 small nucleolar RNA-associated protein 10


Mass: 49044.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#22: Protein U3 small nucleolar RNA-associated protein 4


Mass: 84357.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#24: Protein U3 small nucleolar RNA-associated protein 6


Mass: 46689.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#25: Protein U3 small nucleolar RNA-associated protein 12


Mass: 104697.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#26: Protein U3 small nucleolar RNA-associated protein 18 / U3 snoRNA-associated protein 18 / U three protein 18


Mass: 66494.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40362
#27: Protein U3 small nucleolar RNA-associated protein 21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 102793.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06078
#30: Protein U3 small nucleolar RNA-associated protein 7 / U3 snoRNA-associated protein 7 / U three protein 7


Mass: 48731.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40055
#46: Protein U3 small nucleolar RNA-associated protein 14


Mass: 21558.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#48: Protein U3 small nucleolar RNA-associated protein 11 / U3 snoRNA-associated protein 11 / U three protein 11


Mass: 29604.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B5VM59
#51: Protein U3 small nucleolar RNA-associated protein 22 / U3 snoRNA-associated protein 22 / U three protein 22


Mass: 130146.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53254
#55: Protein U3 small nucleolar RNA-associated protein 8 / U3 snoRNA-associated protein 8 / U three protein 8 / U3 protein 8 required for transcription / t-UTP8


Mass: 77467.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53276
#57: Protein U3 small nucleolar RNA-associated protein 13 / U3 snoRNA-associated protein 13 / U three protein 13


Mass: 90455.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05946
#61: Protein U3 small nucleolar RNA-associated protein 20 / U3 snoRNA-associated protein 20 / U three protein 20


Mass: 278852.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35194

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Nucleolar protein ... , 2 types, 2 molecules SASB

#2: Protein Nucleolar protein 56 / Nucleolus


Mass: 45461.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#59: Protein Nucleolar protein 58 / Nucleolus / Nucleolar protein 5


Mass: 47808.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZPE5

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Protein , 19 types, 23 molecules NBLHLOLUNKSCSDSESFSGSHSJSKSOSZNJNINDNESVLYLX5

#3: Protein Something about silencing protein 10


Mass: 20009.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#17: Protein NET1-associated nuclear protein 1


Mass: 100911.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#23: Protein Periodic tryptophan protein 2 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1


Mass: 96434.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25635
#28: Protein Protein SOF1 / U3 small nucleolar RNA-associated protein SOF1 / U3 snoRNA-associated protein SOF1


Mass: 53819.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33750
#33: Protein KRR1 small subunit processome component / / KRR-R motif-containing protein 1 / Ribosomal RNA assembly protein KRR1


Mass: 20170.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25586
#34: Protein rRNA 2'-O-methyltransferase fibrillarin / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / Nucleolar ...Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / Nucleolar protein 1 / U3 snoRNA-associated protein NOP1


Mass: 27341.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#35: Protein Ribonucloprotein


Mass: 13083.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PW82
#36: Protein RRP9 isoform 1


Mass: 52527.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4BU80
#37: Protein RNA 3'-terminal phosphate cyclase-like protein


Mass: 39588.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08096
#39: Protein Ribosomal RNA small subunit methyltransferase NEP1 / / 18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / ...18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / Essential for mitotic growth protein 1 / Nucleolar essential protein 1


Mass: 26190.480 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#43: Protein Pre-rRNA-processing protein PNO1 / Partner of NOB1 / Ribosomal RNA-processing protein 20


Mass: 20189.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q99216
#49: Protein Essential nuclear protein 1


Mass: 29998.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38333
#50: Protein rRNA biogenesis protein RRP5 / Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA- ...Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA-associated protein RRP5


Mass: 30781.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05022
#52: Protein Ribosomal RNA-processing protein 7


Mass: 21532.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25368
#56: Protein Bud site selection protein 21 / U three protein 16 / U3 small nucleolar RNA-associated protein 16 / U3 snoRNA-associated protein 16


Mass: 7070.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08492
#58: Protein Protein FAF1 / Forty S assembly factor


Mass: 27095.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40546
#60: Protein Regulator of rDNA transcription protein 14


Mass: 10916.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40470
#62: Protein RNA cytidine acetyltransferase / 18S rRNA cytosine acetyltransferase / Killer toxin-resistance protein 33 / Ribosomal RNA cytidine ...18S rRNA cytosine acetyltransferase / Killer toxin-resistance protein 33 / Ribosomal RNA cytidine acetyltransferase 1


Mass: 104469.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P53914, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#65: Protein Protein BFR2 / Brefeldin A resistance protein 2


Mass: 61285.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06631

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RNA chain , 3 types, 3 molecules L0L28

#4: RNA chain 5' ETS


Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 831416132
#5: RNA chain U3 snoRNA


Mass: 106503.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 751247007
#53: RNA chain 18S pre-rRNA


Mass: 582052.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 874346701

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40S ribosomal protein ... , 15 types, 15 molecules L3L4L5L7L8L9LCLDLELFLGNGSRL6NF

#6: Protein 40S ribosomal protein S18-A / Ribosome


Mass: 14516.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#7: Protein 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 25662.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX35
#8: Protein 40S ribosomal protein S5 / / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


Mass: 23756.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783
#9: Protein 40S ribosomal protein S7-A / Ribosome / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26786
#10: Protein 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX39
#11: Protein 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 20093.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#12: Protein 40S ribosomal protein S16-A / Ribosome / RP61R / Small ribosomal subunit protein uS9-A


Mass: 13798.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX51
#13: Protein 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX47
#14: Protein 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14260.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1
#15: Protein 40S ribosomal protein S24-A / Ribosome / RP50 / Small ribosomal subunit protein eS24-A


Mass: 10130.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX31
#16: Protein 40S ribosomal protein S28-A / Ribosome / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7X9
#32: Protein 40S ribosomal protein S14-B / Ribosome / RP59B / Small ribosomal subunit protein uS11-B


Mass: 11645.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39516
#45: Protein 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 11280.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX29
#63: Protein 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 25123.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX37
#64: Protein 40S ribosomal protein S13 / / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 14164.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756

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Ribosome biogenesis protein ... , 3 types, 3 molecules LVSISN

#29: Protein Ribosome biogenesis protein ENP2 / / Essential nuclear protein 2


Mass: 41373.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48234
#38: Protein Ribosome biogenesis protein BMS1 /


Mass: 127889.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#42: Protein Ribosome biogenesis protein UTP30 / / U3 snoRNP-associated protein UTP30


Mass: 28576.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36144

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U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules LZSM6

#31: Protein U3 small nucleolar ribonucleoprotein protein IMP3 / U3 snoRNP protein IMP3 / Interacting with MPP10 protein 3


Mass: 21797.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32899
#41: Protein U3 small nucleolar ribonucleoprotein protein IMP4 / U3 snoRNP protein IMP4 / Interacting with MPP10 protein 4


Mass: 33536.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53941
#66: Protein U3 small nucleolar ribonucleoprotein protein LCP5


Mass: 40864.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40079

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RRNA-processing protein ... , 2 types, 2 molecules SLSQ

#40: Protein rRNA-processing protein FCF1 / FAF1-copurifying factor 1


Mass: 21003.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05498
#44: Protein rRNA-processing protein FCF2 / FAF1 copurifying factor 2


Mass: 20139.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12035

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Nucleolar complex protein ... , 2 types, 2 molecules STSU

#47: Protein Nucleolar complex protein 14


Mass: 89734.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#54: Protein Nucleolar complex protein 4 / U three protein 19 / U3 small nucleolar RNA-associated protein 19 / U3 snoRNA-associated protein 19


Mass: 59433.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06512

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Details

Sequence detailsResidues for which the identity and register can not be assigned are listed as UNK. The actual ...Residues for which the identity and register can not be assigned are listed as UNK. The actual sequences can be found under the following UniProt ids: chain L3 - P0CX55, LH - Q02931, LK - P38882, LM - P42945, LN - Q06679, LP - Q02354, LQ - Q12220, NB - Q12136, SA Q12460, SI - Q08965, SS - Q04500, ST - Q99207.

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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: Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.7
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: 1300 nm
Image recordingElectron dose: 1.074 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199534 / Symmetry type: POINT

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