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- PDB-6ke6: 3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome -

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Basic information

Entry
Database: PDB / ID: 6ke6
Title3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome
Components
  • (40S ribosomal protein ...) x 18
  • (Nucleolar complex protein ...) x 2
  • (Nucleolar protein ...Nucleolus) 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 rRNA18S ribosomal RNA
  • 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 FAF1
  • Protein SOF1
  • RNA 3'-terminal phosphate cyclase-like protein
  • RNA cytidine acetyltransferase
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Something about silencing protein 10
  • U3 snoRNA
  • Unassigned helices
  • rRNA 2'-O-methyltransferase fibrillarin
KeywordsRIBOSOME / ribosome assembly / 90S pre-ribosome / cryo-EM / Mtr4
Function / homology
Function and homology information


rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / CURI complex / sno(s)RNA processing / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process / t-UTP complex ...rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / CURI complex / sno(s)RNA processing / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing / Mpp10 complex / septum digestion after cytokinesis / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA modification / rRNA 2'-O-methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / nuclear microtubule / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / snRNA binding / rRNA primary transcript binding / box C/D RNP complex / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / protein localization to nucleolus / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / mTORC1-mediated signalling / histone glutamine methylation / U4 snRNA binding / SUMOylation of RNA binding proteins / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / rRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / poly(A)+ mRNA export from nucleus / tRNA export from nucleus / 90S preribosome / O-methyltransferase activity / preribosome, small subunit precursor / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / snoRNA binding / rRNA methylation / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / enzyme activator activity / translational termination / maintenance of translational fidelity / positive regulation of translational fidelity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / cell cycle / translation / ATP hydrolysis activity / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion
Similarity search - Function
Utp14 protein / Nucleolar protein 10/Enp2 / NUC153 domain / NUC153 / U3 small nucleolar RNA-associated protein 8 / Utp8 family / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain ...Utp14 protein / Nucleolar protein 10/Enp2 / NUC153 domain / NUC153 / U3 small nucleolar RNA-associated protein 8 / Utp8 family / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Helicase / Domain of unknown function (DUF1726) / TmcA/NAT10/Kre33 / Ribosomal RNA assembly KRR1 / Nucleolar complex protein 4 / Down-regulated in metastasis / U3 snoRNA associated / Down-regulated-in-metastasis protein / U3 snoRNA associated / CBF/Mak21 family / CCAAT-binding factor / Nucleolar protein 14 / Nop14-like family / rRNA-processing protein Fcf1, PIN domain / BING4CT (NUC141) domain / Nrap protein PAP/OAS1-like domain 5 / Nrap protein, domain 6 / Fcf2 pre-rRNA processing / Nrap protein domain 6 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein domain 3 / Nrap protein PAP/OAS-like domain / Small-subunit processome, Utp11 / NOL6/Upt22 / Nrap protein, domain 5 / Sof1-like protein / Nrap protein, domain 4 / Nrap protein, domain 3 / Nrap protein, domain 2 / Sof1-like domain / BING4, C-terminal domain / Nrap protein domain 1 / BING4CT (NUC141) domain / Fcf2/DNTTIP2 / Utp11 protein / Fcf2 pre-rRNA processing, C-terminal / Nrap protein domain 1 / WD repeat-containing protein WDR46/Utp7 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Ribosomal RNA-processing protein 7 / Ribosomal RNA-processing protein 7, C-terminal domain / Rrp7 RRM-like N-terminal domain / Rrp7, RRM-like N-terminal domain / UTP15 C terminal / U3 small nucleolar RNA-associated protein 6 / rRNA-processing protein Fcf1/Utp23 / U3 small nucleolar RNA-associated protein 15, C-terminal / U3 small nucleolar RNA-associated protein 6 / Fcf1 / Small-subunit processome, Utp14 / Sas10 C-terminal domain / Sas10 C-terminal domain / NOP5NT (NUC127) domain / NOP5, N-terminal / Ribosome biogenesis protein Bms1, N-terminal / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase-like, conserved site / Utp13 specific WD40 associated domain / Small-subunit processome, Utp13 / Krr1, KH1 domain / Periodic tryptophan protein 2 / Krr1 KH1 domain / BP28, C-terminal domain / U3 small nucleolar RNA-associated protein 10 / Sas10/Utp3/C1D family / Sas10/Utp3/C1D / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / BP28CT (NUC211) domain / Mpp10 protein / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Ribosomal RNA-processing protein Rrp9-like / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Small-subunit processome, Utp21 / Bystin / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Bystin / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase (RTC), insert domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain
Similarity search - Domain/homology
U3 small nucleolar RNA-associated protein MPP10 / Ribosome biogenesis protein ENP2 / 40S ribosomal protein S12 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 13 / 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 MPP10 / Ribosome biogenesis protein ENP2 / 40S ribosomal protein S12 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 13 / 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-processing protein FCF1 / U3 small nucleolar RNA-associated protein 8 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 4 / RNA 3'-terminal phosphate cyclase-like protein / Bud site selection protein 21 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 / U3 small nucleolar RNA-associated protein 18 / 40S ribosomal protein S22-B / 40S ribosomal protein S28-A / Nucleolar protein 58 / Nucleolar protein 56 / Protein FAF1 / GUANOSINE-5'-TRIPHOSPHATE / U3 small nucleolar ribonucleoprotein protein LCP5 / 40S ribosomal protein S18-A / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S23-A / 40S ribosomal protein S24-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / rRNA 2'-O-methyltransferase fibrillarin / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar RNA-associated protein 11 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 9 / Essential nuclear protein 1 / Ribosome biogenesis protein UTP30 / 40S ribosomal protein S27-A / U3 small nucleolar RNA-associated protein 20 / Protein SOF1 / Ribosomal RNA-processing protein 7 / 40S ribosomal protein S1-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S7-A / 40S ribosomal protein S5 / Periodic tryptophan protein 2 / KRR1 small subunit processome component / Nucleolar complex protein 14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDu, Y. / Ye, K. / An, W.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37010201 China
National Natural Science Foundation of China (NSFC)91940302, 91540201, 31430024 China
CitationJournal: To be published
Title: 3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome
Authors: Du, Y. / An, W. / Qi, S. / Ye, K.
History
DepositionJul 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
3A: U3 snoRNA
5A: 5' ETS
SA: 18S rRNA
SC: 40S ribosomal protein S1-A
SF: 40S ribosomal protein S4-A
SG: 40S ribosomal protein S5
SH: 40S ribosomal protein S6-A
SI: 40S ribosomal protein S7-A
SJ: 40S ribosomal protein S8-A
SK: 40S ribosomal protein S9-A
SM: 40S ribosomal protein S11-A
SN: 40S ribosomal protein S12
SO: 40S ribosomal protein S13
SP: 40S ribosomal protein S14-A
SR: 40S ribosomal protein S16-A
ST: 40S ribosomal protein S18-A
SX: 40S ribosomal protein S22-B
SY: 40S ribosomal protein S23-A
SZ: 40S ribosomal protein S24-A
Sc: 40S ribosomal protein S27-A
Sd: 40S ribosomal protein S28-A
3B: rRNA 2'-O-methyltransferase fibrillarin
3C: rRNA 2'-O-methyltransferase fibrillarin
3D: Nucleolar protein 56
3E: Nucleolar protein 58
3F: Ribosomal RNA-processing protein 9
3G: 13 kDa ribonucleoprotein-associated protein
3H: 13 kDa ribonucleoprotein-associated protein
A4: U3 small nucleolar RNA-associated protein 4
A5: U3 small nucleolar RNA-associated protein 5
A8: U3 small nucleolar RNA-associated protein 8
A9: U3 small nucleolar RNA-associated protein 9
AE: U3 small nucleolar RNA-associated protein 10
AF: U3 small nucleolar RNA-associated protein 15
AG: NET1-associated nuclear protein 1
B1: Periodic tryptophan protein 2
B2: U3 small nucleolar RNA-associated protein 12
B3: U3 small nucleolar RNA-associated protein 13
B8: U3 small nucleolar RNA-associated protein 18
BE: U3 small nucleolar RNA-associated protein 21
B6: U3 small nucleolar RNA-associated protein 6
5B: Bud site selection protein 21
5C: U3 small nucleolar RNA-associated protein 7
5D: U3 small nucleolar RNA-associated protein 11
5E: U3 small nucleolar RNA-associated protein MPP10
5F: U3 small nucleolar ribonucleoprotein protein IMP3
5G: U3 small nucleolar ribonucleoprotein protein IMP4
5H: Something about silencing protein 10
5I: Protein SOF1
5J: rRNA-processing protein FCF2
5K: rRNA-processing protein FCF1
RA: Ribosome biogenesis protein ENP2
RB: U3 small nucleolar ribonucleoprotein protein LCP5
RC: KRR1 small subunit processome component
RE: U3 small nucleolar RNA-associated protein 22
RF: Ribosomal RNA-processing protein 7
RG: Ribosomal RNA small subunit methyltransferase NEP1
RH: Ribosomal RNA small subunit methyltransferase NEP1
RI: Ribosome biogenesis protein UTP30
RJ: Ribosome biogenesis protein BMS1
RK: RNA 3'-terminal phosphate cyclase-like protein
RL: RNA cytidine acetyltransferase
RM: RNA cytidine acetyltransferase
RN: Nucleolar complex protein 14
RO: Nucleolar complex protein 4
RP: U3 small nucleolar RNA-associated protein 20
RQ: U3 small nucleolar RNA-associated protein 14
RS: Essential nuclear protein 1
RT: Pre-rRNA-processing protein PNO1
RV: Protein FAF1
X1: Unassigned helices
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,679,13575
Polymers4,678,45771
Non-polymers6784
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 3A5ASA

#1: RNA chain U3 snoRNA


Mass: 106503.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#2: RNA chain 5' ETS


Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#3: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 582052.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c

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40S ribosomal protein ... , 18 types, 18 molecules SCSFSGSHSISJSKSMSNSOSPSRSTSXSYSZScSd

#4: Protein 40S ribosomal protein S1-A / Ribosome / RP10A


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33442
#5: Protein 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26783
#7: Protein 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX37
#8: Protein 40S ribosomal protein S7-A / Ribosome / RP30 / RP40


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26786
#9: Protein 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#10: Protein 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O13516
#11: Protein 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#12: Protein 40S ribosomal protein S12 /


Mass: 15488.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P48589
#13: Protein 40S ribosomal protein S13 / / Rps13 / S27a / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05756
#14: Protein 40S ribosomal protein S14-A / Ribosome / Rps14 / RP59A


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P06367
#15: Protein 40S ribosomal protein S16-A / Ribosome / Rps16 / RP61R


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#16: Protein 40S ribosomal protein S18-A / Ribosome / Rps18 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX55
#17: Protein 40S ribosomal protein S22-B / Ribosome / Rps22 / RP50 / S24 / Small ribosomal subunit protein uS8-B / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E7Y3
#18: Protein 40S ribosomal protein S23-A / Ribosome / Rps23 / RP37 / S28 / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#19: Protein 40S ribosomal protein S24-A / Ribosome / Rps24 / RP50


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#20: Protein 40S ribosomal protein S27-A / Ribosome / Rps27 / RP61 / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35997
#21: Protein 40S ribosomal protein S28-A / Ribosome / Rps28 / S33 / YS27


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9

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Protein , 15 types, 19 molecules 3B3C3G3HAGB15B5H5IRCRGRHRKRLRMRSRTRVX1

#22: Protein rRNA 2'-O-methyltransferase fibrillarin / Nop1 / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 ...Nop1 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#26: Protein 13 kDa ribonucleoprotein-associated protein / Snu13 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39990
#33: Protein NET1-associated nuclear protein 1 / Utp17 / U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar ...Utp17 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02931
#34: Protein Periodic tryptophan protein 2 / Utp1 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25635
#40: Protein Bud site selection protein 21 / Bud21 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08492
#46: Protein Something about silencing protein 10 / Sas10 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12136
#47: Protein Protein SOF1 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33750
#52: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25586
#55: Protein Ribosomal RNA small subunit methyltransferase NEP1 / / Emg1 / 18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / ...Emg1 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#58: Protein RNA 3'-terminal phosphate cyclase-like protein / Rcl1


Mass: 40220.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08096
#59: Protein RNA cytidine acetyltransferase / Kre33 / 18S rRNA cytosine acetyltransferase / Killer toxin-resistance protein 33 / Ribosomal RNA ...Kre33 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P53914, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#64: Protein Essential nuclear protein 1 / Enp1


Mass: 55207.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38333
#65: Protein Pre-rRNA-processing protein PNO1


Mass: 36356.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#66: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40546
#67: Protein Unassigned helices


Mass: 29549.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c

+
Nucleolar protein ... , 2 types, 2 molecules 3D3E

#23: Protein Nucleolar protein 56 / Nucleolus / Nop56 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12460
#24: Protein Nucleolar protein 58 / Nucleolus / Nucleolar protein 5


Mass: 57060.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12499

+
Ribosomal RNA-processing protein ... , 2 types, 2 molecules 3FRF

#25: Protein Ribosomal RNA-processing protein 9 / Rrp9


Mass: 65146.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06506
#54: Protein Ribosomal RNA-processing protein 7 / Rrp7


Mass: 34526.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25368

+
U3 small nucleolar RNA-associated protein ... , 17 types, 17 molecules A4A5A8A9AEAFB2B3B8BEB65C5D5ERERPRQ

#27: Protein U3 small nucleolar RNA-associated protein 4 / Utp4 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06679
#28: Protein U3 small nucleolar RNA-associated protein 5 / Utp5 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04177
#29: Protein U3 small nucleolar RNA-associated protein 8 / Utp8 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53276
#30: Protein U3 small nucleolar RNA-associated protein 9 / Utp9 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38882
#31: Protein U3 small nucleolar RNA-associated protein 10 / Utp10 / U3 snoRNA-associated protein 10 / U three protein 10 / U3 protein 10 required for ...Utp10 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P42945
#32: Protein U3 small nucleolar RNA-associated protein 15 / Utp15 / U3 snoRNA-associated protein 15 / U three protein 15 / U3 protein 15 required for ...Utp15 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04305
#35: Protein U3 small nucleolar RNA-associated protein 12 / Utp12 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12220
#36: Protein U3 small nucleolar RNA-associated protein 13 / Utp13 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05946
#37: Protein U3 small nucleolar RNA-associated protein 18 / Utp18 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40362
#38: Protein U3 small nucleolar RNA-associated protein 21 / Utp21 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06078
#39: Protein U3 small nucleolar RNA-associated protein 6 / Utp6 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02354
#41: Protein U3 small nucleolar RNA-associated protein 7 / Utp7 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40055
#42: Protein U3 small nucleolar RNA-associated protein 11 / Utp11 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P34247
#43: Protein U3 small nucleolar RNA-associated protein MPP10 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P47083
#53: Protein U3 small nucleolar RNA-associated protein 22 / Utp22 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53254
#62: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35194
#63: Protein U3 small nucleolar RNA-associated protein 14 / Utp14 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04500

+
U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules 5F5GRB

#44: Protein U3 small nucleolar ribonucleoprotein protein IMP3 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32899
#45: Protein U3 small nucleolar ribonucleoprotein protein IMP4 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53941
#51: Protein U3 small nucleolar ribonucleoprotein protein LCP5 / Lcp5


Mass: 40864.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40079

+
RRNA-processing protein ... , 2 types, 2 molecules 5J5K

#48: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12035
#49: Protein rRNA-processing protein FCF1 / Utp24 / FAF1-copurifying factor 1


Mass: 21650.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05498

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

#50: Protein Ribosome biogenesis protein ENP2 / / Enp2 / Essential nuclear protein 2


Mass: 81864.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P48234
#56: Protein Ribosome biogenesis protein UTP30 / / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36144
#57: Protein Ribosome biogenesis protein BMS1 / / Bms1


Mass: 135792.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08965

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

#60: Protein Nucleolar complex protein 14 / Nop14 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q99207
#61: Protein Nucleolar complex protein 4 / Noc4 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06512

+
Non-polymers , 3 types, 4 molecules

#68: Chemical ChemComp-ZN / ZINC ION / Zinc


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


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#70: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

+
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 90S pre-ribosome (Mtr4-depleted, Enp1-TAP) / Type: COMPLEX / Entity ID: #1-#67 / Source: NATURAL
Molecular weightValue: 5 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMpotassium acetateCH3COOK1
220 mMHEPES-KHEPES-K1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: wait 30s and blot 2s before plunging

-
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 magnification: 25000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 9.3 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 4723
Image scansMovie frames/image: 32 / Used frames/image: 1-32

-
Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1.8CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 154939
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121139 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-ID
15WYJ1
25WLC1

+
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