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- PDB-9n74: SSU processome maturation and disassembly, State H -

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Basic information

Entry
Database: PDB / ID: 9n74
TitleSSU processome maturation and disassembly, State H
Components
  • (40S ribosomal protein ...) x 18
  • (Nucleolar complex protein ...) x 2
  • (Nucleolar protein ...) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 17
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • (rRNA-processing protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • 18S rRNA
  • 5'ETS rRNA
  • Bud site selection protein 21
  • Dimethyladenosine transferase
  • Essential nuclear protein 1
  • Exosome complex exonuclease RRP6
  • NET1-associated nuclear protein 1
  • Periodic tryptophan protein 2
  • Pre-rRNA-processing protein PNO1
  • Probable ATP-dependent RNA helicase DHR1
  • Protein SOF1
  • RNA 3'-terminal phosphate cyclase-like protein
  • Regulator of rDNA transcription protein 14
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Ribosome biogenesis protein BMS1
  • Small ribosomal subunit protein eS1A
  • Something about silencing protein 10
  • U3 snoRNA
  • Ubiquitin-40S ribosomal protein S31
  • Unassigned peptides
  • 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


18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / regulation of ribosomal protein gene transcription by RNA polymerase II / U1 snRNA 3'-end processing / rRNA small subunit pseudouridine methyltransferase Nep1 / box H/ACA snoRNA binding ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / regulation of ribosomal protein gene transcription by RNA polymerase II / U1 snRNA 3'-end processing / rRNA small subunit pseudouridine methyltransferase Nep1 / box H/ACA snoRNA binding / nuclear polyadenylation-dependent CUT catabolic process / RNA fragment catabolic process / U5 snRNA 3'-end processing / Noc4p-Nop14p complex / rRNA 2'-O-methylation / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / CURI complex / UTP-C complex / U4 snRNA 3'-end processing / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear microtubule / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / Mpp10 complex / nuclear exosome (RNase complex) / rRNA (pseudouridine) methyltransferase activity / rRNA modification / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA binding / regulation of rRNA processing / septum digestion after cytokinesis / tRNA re-export from nucleus / snRNA binding / rRNA (adenine-N6,N6-)-dimethyltransferase activity / histone mRNA catabolic process / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / rDNA heterochromatin / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / 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) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / 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 / 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 / rRNA methylation / Protein hydroxylation / RNA catabolic process / U4 snRNP / regulation of telomere maintenance / poly(U) RNA binding / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / preribosome, small subunit precursor / precatalytic spliceosome / 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 / ribosomal subunit export from nucleus / RNA processing / regulation of translational fidelity / 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) / U4/U6 x U5 tri-snRNP complex
Similarity search - Function
Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / U3 small nucleolar RNA-associated protein 8 / : / Utp8, N-terminal beta propeller / Utp8, C-terminal ...Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / U3 small nucleolar RNA-associated protein 8 / : / Utp8, N-terminal beta propeller / Utp8, C-terminal / rRNA biogenesis protein Rrp5 / : / : / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 snoRNA associated / U3 small nucleolar RNA-associated protein 20, C-terminal / : / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 snoRNA associated / U3 small nucleolar RNA-associated protein 20 domain / Small subunit processome component 20 homolog, C-terminal / Nucleolar complex protein 4 / WD repeat-containing protein 75 second beta-propeller / Nucleolar protein 14 / Nop14-like family / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Nrap protein domain 1 / 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 / 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 4 / : / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Small-subunit processome, Utp11 / Sof1-like protein / BING4, C-terminal domain / Fcf2 pre-rRNA processing, C-terminal / Fcf2/DNTTIP2 / WD repeat-containing protein WDR46/Utp7 / : / : / Utp11 protein / Sof1-like domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing / BING4CT (NUC141) domain / : / U3 small nucleolar RNA-associated protein 15, C-terminal / rRNA-processing protein Fcf1, PIN domain / UTP15 C terminal / Small-subunit processome, Utp14 / Utp14 protein / rRNA-processing protein Fcf1/Utp23 / Sas10 C-terminal domain / Fcf1 / Sas10 C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / BP28, C-terminal domain / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / : / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / HEATR1-like, HEAT repeats / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosome biogenesis protein Bms1, N-terminal / Dip2/Utp12 Family / RNA 3'-terminal phosphate cyclase signature. / : / Small-subunit processome, Utp21 / Utp21 specific WD40 associated putative domain / WDR36/Utp21 second beta-propeller domain / WDR36/Utp21 first beta-propeller / Ribosomal RNA-processing protein Rrp9-like / Sas10/Utp3/C1D / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 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'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / 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 / 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 / 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 RNA-associated protein 18 / Regulator of rDNA transcription protein 14 / Dimethyladenosine transferase / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / Small ribosomal subunit protein eS12 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 8 / 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 / Probable ATP-dependent RNA helicase DHR1 / 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 / 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 / Exosome complex exonuclease RRP6 / 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: 2.65 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: To Be Published
Title: Mechanism of helicase-mediated SSU processome maturation and disassembly
Authors: Buzovetsky, O. / Klinge, S.
History
DepositionFeb 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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: U3 snoRNA
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
LW: U3 small nucleolar RNA-associated protein 7
LZ: U3 small nucleolar ribonucleoprotein protein IMP3
NA: U3 small nucleolar RNA-associated protein MPP10
NB: Something about silencing protein 10
ND: Bud site selection protein 21
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
NL: Dimethyladenosine transferase
NM: Small ribosomal subunit protein eS1A
NP: 40S ribosomal protein S19-A
NQ: 40S ribosomal protein S27-A
NS: Probable ATP-dependent RNA helicase DHR1
NV: Exosome complex exonuclease RRP6
OA: rRNA biogenesis protein RRP5
OH: 40S ribosomal protein S12
OU: Ubiquitin-40S ribosomal protein S31
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
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
SX: Unassigned peptides
SY: U3 small nucleolar RNA-associated protein 11
SZ: Essential nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,693,692116
Polymers4,691,09171
Non-polymers2,60245
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: 329138943
#2: RNA chain 18S rRNA


Mass: 580701.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741
#3: RNA chain U3 snoRNA


Mass: 106943.469 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 ... , 18 types, 18 molecules L3L4L5L6L7L8L9LCLDLELFLGNFNGNPNQOHSR

#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
#35: 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
#36: 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
#41: Protein 40S ribosomal protein S19-A / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P07280
#42: 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
#46: Protein 40S ribosomal protein S12


Mass: 15488.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P48589
#60: 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 , 19 types, 22 molecules LHLOLUNBNDNLNMNSNVOAOUSCSDSESFSHSISJSKSVSWSZ

#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: 104097.039 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
#33: 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
#34: 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
#39: Protein Dimethyladenosine transferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / 18S rRNA dimethylase / S- ...18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / 18S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 36003.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741
References: UniProt: P41819, 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
#40: 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
#43: Protein Probable ATP-dependent RNA helicase DHR1 / DEAH box RNA helicase DHR1 / Extracellular mutant protein 16


Mass: 145171.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q04217, RNA helicase
#44: Protein Exosome complex exonuclease RRP6 / Rrp6p / Ribosomal RNA-processing protein 6


Mass: 84160.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741
References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#45: 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
#47: Protein Ubiquitin-40S ribosomal protein S31


Mass: 17254.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P05759
#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
#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
#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
#64: 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
#65: 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
#30: 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
#32: 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
#37: 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
#58: 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
#61: Protein U3 small nucleolar RNA-associated protein 14 / U3 snoRNA-associated protein 14 / U three protein 14


Mass: 103269.727 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

+
U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules LZSM

#31: 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
#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

#38: 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
#59: 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

#62: 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
#63: 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

+
Protein/peptide , 1 types, 1 molecules SX

#66: Protein/peptide Unassigned peptides


Mass: 2672.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741

+
Non-polymers , 5 types, 45 molecules

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


Mass: 24.305 Da / Num. of mol.: 39 / 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.: 3 / Source method: obtained synthetically / Formula: Zn
#72: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#73: 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 H / Type: COMPLEX / Entity ID: #1-#68 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
160 mMTris-HCl1
250 mMNaCl1
35 mMMgCl1
42 %glycerol1
50.01 %NP-401
61 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 61.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 328554 / Symmetry type: POINT

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