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- PDB-9n6x: SSU processome maturation and disassembly, State B -

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Basic information

Entry
Database: PDB / ID: 9n6x
TitleSSU processome maturation and disassembly, State B
Components
  • (40S ribosomal protein ...) x 16
  • (Nucleolar complex protein ...) x 2
  • (Nucleolar protein ...) x 2
  • (Ribosomal RNA-processing protein ...) 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
  • 13 kDa ribonucleoprotein-associated protein
  • 18S rRNA
  • 5'ETS rRNA
  • 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
  • Regulator of rDNA transcription protein 14
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Small ribosomal subunit protein eS1A
  • Something about silencing protein 10
  • TPA: Saccharomyces cerevisiae U3a gene for small nucleolar RNA U3a
  • rRNA 2'-O-methyltransferase fibrillarin
  • rRNA biogenesis protein RRP5
KeywordsRIBOSOME / SSU processome / ribosome assembly / RNA folding / RNA-protein interactions
Function / homology
Function and homology information


tRNA wobble cytosine modification / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / tRNA acetylation / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex ...tRNA wobble cytosine modification / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / tRNA acetylation / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Noc4p-Nop14p complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / box C/D sno(s)RNA binding / snoRNA guided rRNA 2'-O-methylation / rRNA modification / histone H2AQ104 methyltransferase activity / septum digestion after cytokinesis / regulation of rRNA processing / tRNA re-export from nucleus / snRNA binding / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / rDNA heterochromatin / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (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 / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / rRNA primary transcript binding / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / U4 snRNA binding / O-methyltransferase activity / SUMOylation of RNA binding proteins / protein localization to nucleolus / 90S preribosome assembly / mTORC1-mediated signalling / mRNA modification / rRNA methylation / Protein hydroxylation / U4 snRNP / poly(U) RNA binding / U3 snoRNA 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 / Ribosomal scanning and start codon recognition / snoRNA binding / precatalytic spliceosome / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / establishment of cell polarity / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / Ub-specific processing proteases / proteasome assembly / RNA processing / regulation of translational fidelity / ribosomal subunit export from nucleus / U4/U6 x U5 tri-snRNP complex / ribosomal small subunit export from nucleus / vesicle-mediated transport / 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) / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA / spliceosomal complex / small-subunit processome / translational initiation / enzyme activator activity / mRNA splicing, via spliceosome / maintenance of translational fidelity / rRNA processing
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 / Nucleolar protein 10-like, second domain / Nucleolar protein 10-like, N-terminal domain / rRNA biogenesis protein Rrp5 / : / : / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / U3 small nucleolar RNA-associated protein 8 / : / Utp8, N-terminal beta propeller / Utp8, C-terminal / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10/TcmA, helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / U3 snoRNA associated / U3 snoRNA associated / Sof1-like protein / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20, C-terminal / : / : / Sof1-like domain / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20 domain / Small subunit processome component 20 homolog, C-terminal / WD repeat-containing protein 75 second beta-propeller / NOL6/Upt22 / BING4, C-terminal domain / Nucleolar complex protein 4 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / WD repeat-containing protein WDR46/Utp7 / Nrap protein domain 1 / BING4CT (NUC141) domain / 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 / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / : / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 4 / Small-subunit processome, Utp11 / Nucleolar protein 14 / Fcf2 pre-rRNA processing, C-terminal / Fcf2/DNTTIP2 / : / Utp11 protein / Nop14-like family / Fcf2 pre-rRNA processing / : / U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / rRNA-processing protein Fcf1, PIN domain / WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / Small-subunit processome, Utp14 / U3 small nucleolar RNA-associated protein 18 / Utp14 protein / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / BP28, C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / :
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / 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 / Small ribosomal subunit protein uS13A / 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 / Small ribosomal subunit protein eS1A / Protein SOF1 / U3 small nucleolar RNA-associated protein 11 / U3 small nucleolar RNA-associated protein 20 / Small ribosomal subunit protein eS27A / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / 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 10 / 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 6 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 14 / 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 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / Protein BFR2 / U3 small nucleolar RNA-associated protein 4 / rRNA processing protein RCL1 / U3 small nucleolar RNA-associated protein 16 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / Small ribosomal subunit protein eS28A / Nucleolar complex protein 14 / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsBuzovetsky, O. / Klinge, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM145950-03 United States
Chan Zuckerberg Initiative2023-332391 United States
CitationJournal: Nature / Year: 2025
Title: Helicase-mediated mechanism of SSU processome maturation and disassembly.
Authors: Olga Buzovetsky / Sebastian Klinge /
Abstract: Eukaryotic ribosomal small subunit (SSU) assembly requires the SSU processome, a nucleolar precursor containing the RNA chaperone U3 small nucleolar RNA (snoRNA). The underlying molecular mechanisms ...Eukaryotic ribosomal small subunit (SSU) assembly requires the SSU processome, a nucleolar precursor containing the RNA chaperone U3 small nucleolar RNA (snoRNA). The underlying molecular mechanisms of SSU processome maturation, remodelling, disassembly and RNA quality control, and the transitions between states remain unknown owing to a paucity of intermediates. Here we report 16 native SSU processome structures alongside genetic data, revealing how two helicases, the Mtr4-exosome and Dhr1, are controlled for accurate and unidirectional ribosome biogenesis. Our data show how irreversible pre-ribosomal RNA degradation by the redundantly tethered RNA exosome couples the transformation of the SSU processome into a pre-40S particle, during which Utp14 can probe evolving surfaces, ultimately positioning and activating Dhr1 to unwind the U3 snoRNA and initiate nucleolar pre-40S release. This study highlights a paradigm for large dynamic RNA-protein complexes in which irreversible RNA degradation drives compositional changes and communicates these changes to govern enzyme activity while maintaining overall quality control.
History
DepositionFeb 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L0: 5'ETS rRNA
L1: 18S rRNA
L2: TPA: Saccharomyces cerevisiae U3a gene for small nucleolar RNA U3a
L3: 40S ribosomal protein S18-A
L4: 40S ribosomal protein S4-A
L5: 40S ribosomal protein S5
L6: 40S ribosomal protein S6-A
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
LI: U3 small nucleolar RNA-associated protein 8
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
LR: U3 small nucleolar RNA-associated protein 13
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
LX: RNA cytidine acetyltransferase
LY: RNA cytidine acetyltransferase
LZ: U3 small nucleolar ribonucleoprotein protein IMP3
NA: U3 small nucleolar RNA-associated protein MPP10
NB: Something about silencing protein 10
NC: U3 small nucleolar ribonucleoprotein protein LCP5
ND: Bud site selection protein 21
NE: Protein FAF1
NF: 40S ribosomal protein S13
NG: 40S ribosomal protein S14-A
NH: U3 small nucleolar RNA-associated protein 22
NI: Ribosomal RNA-processing protein 7
NK: KRR1 small subunit processome component
NM: Small ribosomal subunit protein eS1A
NN: Protein BFR2
NQ: 40S ribosomal protein S27-A
OA: rRNA biogenesis protein RRP5
SA: Nucleolar protein 56
SB: Nucleolar protein 58
SC: rRNA 2'-O-methyltransferase fibrillarin
SD: rRNA 2'-O-methyltransferase fibrillarin
SE: 13 kDa ribonucleoprotein-associated protein
SF: 13 kDa ribonucleoprotein-associated protein
SG: Ribosomal RNA-processing protein 9
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
SP: U3 small nucleolar RNA-associated protein 20
SQ: rRNA-processing protein FCF2
SR: 40S ribosomal protein S23-A
SS: U3 small nucleolar RNA-associated protein 14
ST: Nucleolar complex protein 14
SU: Nucleolar complex protein 4
SV: Regulator of rDNA transcription protein 14
SW: Pre-rRNA-processing protein PNO1
SY: U3 small nucleolar RNA-associated protein 11
SZ: Essential nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,908,515110
Polymers4,906,52772
Non-polymers1,98838
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules L0L1L2

#1: RNA chain 5'ETS rRNA


Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: GenBank: 1262303
#2: RNA chain 18S rRNA


Mass: 582381.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: GenBank: 329138943
#3: RNA chain TPA: Saccharomyces cerevisiae U3a gene for small nucleolar RNA U3a


Mass: 106503.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741

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40S ribosomal protein ... , 16 types, 16 molecules L3L4L5L6L7L8L9LCLDLELFLGNFNGNQSR

#4: Protein 40S ribosomal protein S18-A / Small ribosomal subunit protein uS13-A


Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX55
#5: Protein 40S ribosomal protein S4-A / RP5 / S7 / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX35
#6: Protein 40S ribosomal protein S5 / RP14 / S2 / YS8


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P26783
#7: Protein 40S ribosomal protein S6-A / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX37
#8: Protein 40S ribosomal protein S7-A / RP30 / RP40


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P26786
#9: Protein 40S ribosomal protein S8-A / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX39
#10: Protein 40S ribosomal protein S9-A / RP21 / S13 / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: O13516
#11: Protein 40S ribosomal protein S16-A / RP61R


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX51
#12: Protein 40S ribosomal protein S11-A / RP41 / S18 / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX47
#13: Protein 40S ribosomal protein S22-A / RP50 / S24 / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0C0W1
#14: Protein 40S ribosomal protein S24-A / RP50


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX31
#15: Protein 40S ribosomal protein S28-A / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q3E7X9
#39: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P05756
#40: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P06367
#46: Protein 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P35997
#61: Protein 40S ribosomal protein S23-A / RP37 / S28 / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX29

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Protein , 18 types, 22 molecules LHLOLULXLYNBNDNENKNMNNOASCSDSESFSHSJSKSVSWSZ

#16: Protein NET1-associated nuclear protein 1 / U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar RNA- ...U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar RNA-associated protein 17 / U3 snoRNA-associated protein 17


Mass: 101341.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q02931
#23: Protein Periodic tryptophan protein 2 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1


Mass: 104177.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P25635
#29: Protein Protein SOF1 / U3 small nucleolar RNA-associated protein SOF1 / U3 snoRNA-associated protein SOF1


Mass: 56888.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P33750
#32: 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: 119509.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741
References: UniProt: P53914, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#35: Protein Something about silencing protein 10 / U three protein 3 / U3 small nucleolar RNA-associated protein 3 / U3 snoRNA-associated protein 11


Mass: 70364.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q12136
#37: Protein Bud site selection protein 21 / U three protein 16 / U3 small nucleolar RNA-associated protein 16 / U3 snoRNA-associated protein 16


Mass: 24431.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q08492
#38: Protein Protein FAF1 / Forty S assembly factor


Mass: 38961.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P40546
#43: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P25586
#44: Protein Small ribosomal subunit protein eS1A / 40S ribosomal protein S1-A / RP10A


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P33442
#45: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: Q06631
#47: 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: 193411.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q05022
#50: Protein rRNA 2'-O-methyltransferase fibrillarin / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA- ...Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA-associated protein NOP1


Mass: 34525.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741
References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#51: Protein 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein 1


Mass: 13582.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P39990
#53: Protein RNA 3'-terminal phosphate cyclase-like protein


Mass: 40220.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q08096
#55: 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: 27936.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#65: Protein Regulator of rDNA transcription protein 14


Mass: 23898.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P40470
#66: Protein Pre-rRNA-processing protein PNO1 / Partner of NOB1 / Ribosomal RNA-processing protein 20


Mass: 30380.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q99216
#68: Protein Essential nuclear protein 1


Mass: 55207.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P38333

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

#17: 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: 80269.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P53276
#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 S288C (yeast) / Cell line: BY4741 / References: UniProt: Q04305
#19: Protein U3 small nucleolar RNA-associated protein 9 / U3 snoRNA-associated protein 9 / U three protein 9 / U3 protein 9 required for transcription / t-UTP9


Mass: 65347.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P38882
#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: 72079.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q04177
#21: Protein U3 small nucleolar RNA-associated protein 10 / U3 snoRNA-associated protein 10 / U three protein 10 / U3 protein 10 required for transcription / t-UTP10


Mass: 200298.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P42945
#22: Protein U3 small nucleolar RNA-associated protein 4 / U3 snoRNA-associated protein 4 / U three protein 4 / U3 protein 4 required for transcription / t-UTP4


Mass: 87909.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q06679
#24: Protein U3 small nucleolar RNA-associated protein 6 / U3 snoRNA-associated protein 6 / U three protein 6


Mass: 52495.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q02354
#25: Protein U3 small nucleolar RNA-associated protein 12 / U3 snoRNA-associated protein 12 / DOM34-interacting protein 2 / U three protein 12


Mass: 106481.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q12220
#26: Protein U3 small nucleolar RNA-associated protein 13 / U3 snoRNA-associated protein 13 / U three protein 13


Mass: 91132.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q05946
#27: Protein U3 small nucleolar RNA-associated protein 18 / U3 snoRNA-associated protein 18 / U three protein 18


Mass: 66574.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P40362
#28: Protein U3 small nucleolar RNA-associated protein 21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 104927.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q06078
#31: Protein U3 small nucleolar RNA-associated protein 7 / U3 snoRNA-associated protein 7 / U three protein 7


Mass: 62418.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P40055
#34: Protein U3 small nucleolar RNA-associated protein MPP10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10


Mass: 67042.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P47083
#41: Protein U3 small nucleolar RNA-associated protein 22 / U3 snoRNA-associated protein 22 / U three protein 22


Mass: 140660.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P53254
#59: Protein U3 small nucleolar RNA-associated protein 20 / U3 snoRNA-associated protein 20 / U three protein 20


Mass: 287915.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P35194
#62: Protein U3 small nucleolar RNA-associated protein 14 / U3 snoRNA-associated protein 14 / U three protein 14


Mass: 103189.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q04500
#67: Protein U3 small nucleolar RNA-associated protein 11 / U3 snoRNA-associated protein 11 / U three protein 11


Mass: 29806.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P34247

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

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


Mass: 81864.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P48234
#54: Protein Ribosome biogenesis protein BMS1


Mass: 135792.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q08965
#58: Protein Ribosome biogenesis protein UTP30 / U3 snoRNP-associated protein UTP30


Mass: 31668.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P36144

+
U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules LZNCSM

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


Mass: 21928.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P32899
#36: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P40079
#57: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P53941

+
Ribosomal RNA-processing protein ... , 2 types, 2 molecules NISG

#42: Protein Ribosomal RNA-processing protein 7


Mass: 34526.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P25368
#52: Protein Ribosomal RNA-processing protein 9


Mass: 65146.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q06506

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

#48: Protein Nucleolar protein 56 / Ribosome biosynthesis protein SIK1 / Suppressor of I kappa b protein 1


Mass: 56961.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q12460
#49: Protein Nucleolar protein 58 / Nucleolar protein 5


Mass: 57060.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q12499

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

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


Mass: 21650.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q05498
#60: Protein rRNA-processing protein FCF2 / FAF1 copurifying factor 2


Mass: 25689.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q12035

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

#63: Protein Nucleolar complex protein 14 / U three protein 2 / U3 small nucleolar RNA-associated protein 2 / U3 snoRNA-associated protein 2


Mass: 94463.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q99207
#64: Protein Nucleolar complex protein 4 / U three protein 19 / U3 small nucleolar RNA-associated protein 19 / U3 snoRNA-associated protein 19


Mass: 63707.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q06512

+
Non-polymers , 4 types, 38 molecules

#69: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: Mg
#70: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#71: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#72: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SSU processome maturation and disassembly, State B / Type: RIBOSOME / Entity ID: #1-#68 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
160 mMTris-HCl1
250 mMSodium chlorideNaCl1
35 mMMagnesium chlorideMgCl21
42 %glycerol1
50.01 %NP-401
61 mMDTT1
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28151 / Symmetry type: POINT

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