[English] 日本語
Yorodumi
- PDB-6lqs: Cryo-EM structure of 90S small subunit preribosomes in transition... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lqs
TitleCryo-EM structure of 90S small subunit preribosomes in transition states (State D)
Components
  • (40S ribosomal protein ...) x 16
  • (Exosome complex component ...) x 9
  • (Exosome complex exonuclease ...) x 2
  • (Nucleolar complex protein ...) x 2
  • (Nucleolar protein ...Nucleolus) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 17
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • (Unassigned helices ...) x 2
  • (rRNA-processing protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • 18S pre-rRNA
  • 5' ETS
  • ATP-dependent RNA helicase DOB1
  • Bud site selection protein 21
  • Essential nuclear protein 1
  • Exosome complex protein LRP1
  • M-phase phosphoprotein 6 homolog
  • NET1-associated nuclear protein 1
  • Periodic tryptophan protein 2
  • Pno1
  • 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
  • Something about silencing protein 10
  • U3 snoRNA
  • rRNA 2'-O-methyltransferase fibrillarin
  • rRNA biogenesis protein RRP5
KeywordsRIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1
Function / homology
Function and homology information


regulation of exoribonuclease activity / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / ncRNA polyadenylation / ncRNA 3'-end processing / TRAMP complex / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process ...regulation of exoribonuclease activity / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / ncRNA polyadenylation / ncRNA 3'-end processing / TRAMP complex / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / 3'-5' RNA helicase activity / Noc4p-Nop14p complex / CURI complex / nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' / nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription / t-UTP complex / nuclear retention of unspliced pre-mRNA at the site of transcription / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / cytoplasmic exosome (RNase complex) / UTP-C complex / nuclear retention of pre-mRNA at the site of transcription / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear polyadenylation-dependent mRNA catabolic process / sno(s)RNA processing / U5 snRNA 3'-end processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / nuclear polyadenylation-dependent tRNA catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / nuclear polyadenylation-dependent rRNA catabolic process / box C/D RNA binding / CUT catabolic process / box C/D RNA 3'-end processing / exosome (RNase complex) / U4 snRNA 3'-end processing / nuclear exosome (RNase complex) / Mpp10 complex / box H/ACA snoRNA binding / rRNA methyltransferase activity / polyadenylation-dependent snoRNA 3'-end processing / mRNA 3'-UTR AU-rich region binding => GO:0035925 / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (pseudouridine) methyltransferase activity / septum digestion after cytokinesis / rRNA 2'-O-methylation / rRNA modification / nuclear mRNA surveillance / nuclear-transcribed mRNA catabolic process, non-stop decay / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / rDNA heterochromatin / nuclear microtubule / histone mRNA catabolic process / 90S preribosome assembly / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / snRNA binding / rRNA metabolic process / nonfunctional rRNA decay / rRNA primary transcript binding / rRNA catabolic process / exonucleolytic catabolism of deadenylated mRNA / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / protein localization to nucleolus / maturation of 5.8S rRNA / histone glutamine methylation / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / poly(A) binding / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / RNA catabolic process / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / tRNA export from nucleus / precatalytic spliceosome / 90S preribosome / preribosome, small subunit precursor / O-methyltransferase activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA binding / mRNA catabolic process / poly(U) RNA binding / 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) / maturation of SSU-rRNA / regulation of translational fidelity / U4/U6 x U5 tri-snRNP complex / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / maturation of LSU-rRNA
Nucleolar protein 14 / Small-subunit processome, Utp11 / S15/NS1, RNA-binding / Bystin / Small-subunit processome, Utp21 / Sof1-like protein / Small-subunit processome, Utp12 / Sas10/Utp3/C1D / Brix domain / Quinoprotein alcohol dehydrogenase-like superfamily ...Nucleolar protein 14 / Small-subunit processome, Utp11 / S15/NS1, RNA-binding / Bystin / Small-subunit processome, Utp21 / Sof1-like protein / Small-subunit processome, Utp12 / Sas10/Utp3/C1D / Brix domain / Quinoprotein alcohol dehydrogenase-like superfamily / Ribosome biogenesis protein BMS1/TSR1, C-terminal / rRNA-processing protein Fcf1/Utp23 / Small-subunit processome, Utp14 / Ribosomal protein S12/S23 / KOW / Ribosomal protein S5/S7, eukaryotic/archaeal / HRDC-like superfamily / Exosome-associated factor Rrp47/DNA strand repair C1D / Ribosomal protein S23, eukaryotic/archaeal / Exosome-associated factor Rrp6, N-terminal / BP28, C-terminal domain / BING4, C-terminal domain / AARP2CN / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / Prismane-like superfamily / Ribonuclease H-like superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Tetratricopeptide-like helical domain superfamily / DEAD/DEAH box helicase domain / Down-regulated-in-metastasis protein / Zinc-binding ribosomal protein / Ribosomal protein S4/S9, eukaryotic/archaeal / CCAAT-binding factor / NOP5, N-terminal / Fibrillarin / Ribosomal protein S3Ae / Ribosomal protein S6e / Exoribonuclease, phosphorolytic domain 1 / Ribosomal protein S8e / Ribosomal protein S4e / Ribosomal protein S9 / Ribosomal protein S8 / WD40 repeat / Ribosomal protein S27 / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S28e / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Helicase, C-terminal / Ribonuclease II/R / NOL6/Upt22 / S1 domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / K Homology domain, type 1 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae conserved site / ATPase, AAA-type, core / HAT (Half-A-TPR) repeat / RNA-binding S4 domain / Ribosomal protein S4/S9, N-terminal / PIN domain / Nop domain / 3'-5' exonuclease domain / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / HRDC domain / Ribosomal protein S24e / Ribosomal protein S11 / ATP-dependent RNA helicase Ski2, C-terminal / NOSIC / Exosome complex component Rrp43 / Ribosomal protein S15P / Exosome complex component, N-terminal domain / rRNA-processing arch domain / Anaphase-promoting complex subunit 4, WD40 domain / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal protein S7 domain / RNA 3'-terminal phosphate cyclase domain / RNA-binding domain, S1 / Periodic tryptophan protein 2 / Ribonuclease II/R, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / U3 small nucleolar RNA-associated protein 10, N-terminal / HEAT, type 2 / Fibrillarin, conserved site / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Nucleolar complex protein 4 / Ribosomal protein S7, conserved site / PIN-like domain superfamily / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Regulator of rDNA transcription 14 / Bms1/Tsr1-type G domain / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase / Alpha/beta knot methyltransferases
U3 small nucleolar RNA-associated protein 8 / M-phase phosphoprotein 6 homolog / Exosome complex component CSL4 / 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 14 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 ...U3 small nucleolar RNA-associated protein 8 / M-phase phosphoprotein 6 homolog / Exosome complex component CSL4 / 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 14 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 / Exosome complex component RRP45 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 15 / Nucleolar complex protein 4 / Ribosomal RNA-processing protein 9 / U3 small nucleolar RNA-associated protein 12 / U3 small nucleolar RNA-associated protein 22 / 40S ribosomal protein S22-B / 40S ribosomal protein S28-A / Nucleolar protein 58 / Nucleolar protein 56 / Exosome complex component RRP42 / Exosome complex exonuclease RRP6 / U3 small nucleolar RNA-associated protein 4 / Something about silencing protein 10 / rRNA-processing protein FCF2 / Ribosome biogenesis protein BMS1 / Bud site selection protein 21 / Exosome complex component RRP40 / Exosome complex exonuclease DIS3 / RNA 3'-terminal phosphate cyclase-like protein / Exosome complex component RRP46 / 40S ribosomal protein S1-A / Exosome complex component MTR3 / 40S ribosomal protein S8-A / Periodic tryptophan protein 2 / Ribosomal RNA-processing protein 7 / Exosome complex component RRP43 / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S16-A / 40S ribosomal protein S11-A / 40S ribosomal protein S6-A / 40S ribosomal protein S7-A / 40S ribosomal protein S4-A / 40S ribosomal protein S24-A / 40S ribosomal protein S23-A / 40S ribosomal protein S14-A / 40S ribosomal protein S13 / 40S ribosomal protein S9-A / 40S ribosomal protein S5 / U3 small nucleolar ribonucleoprotein protein IMP3 / U3 small nucleolar RNA-associated protein MPP10 / 13 kDa ribonucleoprotein-associated protein / ATP-dependent RNA helicase DOB1 / Exosome complex component SKI6 / U3 small nucleolar RNA-associated protein 10 / Regulator of rDNA transcription protein 14 / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar RNA-associated protein 9 / Protein SOF1 / Exosome complex protein LRP1 / Exosome complex component RRP4 / Essential nuclear protein 1 / 40S ribosomal protein S27-A / U3 small nucleolar RNA-associated protein 20 / U3 small nucleolar RNA-associated protein 11 / Nucleolar complex protein 14
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDu, Y. / Ye, K.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91940302, 91540201, 31430024, 31325007 China
Chinese Academy of SciencesXDB08010203 China
CitationJournal: Science / Year: 2020
Title: Cryo-EM structure of 90 small ribosomal subunit precursors in transition states.
Authors: Yifei Du / Weidong An / Xing Zhu / Qi Sun / Jia Qi / Keqiong Ye /
Abstract: The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by ...The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of intermediates in the path from the 90 to the pre-40 The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 progression.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0952
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
3A: U3 snoRNA
5A: 5' ETS
SA: 18S pre-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
SO: 40S ribosomal protein S13
SP: 40S ribosomal protein S14-A
SR: 40S ribosomal protein S16-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
RD: rRNA biogenesis protein RRP5
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
RJ: Ribosome biogenesis protein BMS1
RK: RNA 3'-terminal phosphate cyclase-like protein
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: Pno1
RW: Regulator of rDNA transcription protein 14
X1: Unassigned helices 1
X2: Unassigned helices 2
R5: Exosome complex component RRP45
R1: Exosome complex component SKI6
R3: Exosome complex component RRP43
R6: Exosome complex component RRP46
R2: Exosome complex component RRP42
M3: Exosome complex component MTR3
R0: Exosome complex component RRP40
r4: Exosome complex component RRP4
C4: Exosome complex component CSL4
R4: Exosome complex exonuclease DIS3
r6: Exosome complex exonuclease RRP6
R7: Exosome complex protein LRP1
M4: ATP-dependent RNA helicase DOB1
M6: M-phase phosphoprotein 6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,098,03583
Polymers5,097,35679
Non-polymers6784
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
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 pre-rRNA


Mass: 582710.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c

+
40S ribosomal protein ... , 16 types, 16 molecules SCSFSGSHSISJSKSMSOSPSRSXSYSZScSd

#4: Protein 40S ribosomal protein S1-A / Ribosome / Rps1 / 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 / Rps4 / 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 / / Rps5 / 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 / Rps6 / 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 / Rps7 / 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 / Rps8 / 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 / Rps9 / 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 / Rps11 / 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 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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

+
Protein , 17 types, 20 molecules 3B3C3G3HAGB15B5H5IRDRGRHRJRKRSRTRWR7M4M6

#20: 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
#24: 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
#31: 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
#32: Protein Periodic tryptophan protein 2 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1


Mass: 101467.367 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
#38: 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
#44: 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
#45: 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
#48: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05022
#51: 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
#52: 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
#53: 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
#58: Protein Essential nuclear protein 1


Mass: 54879.105 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
#59: 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
#60: Protein Regulator of rDNA transcription protein 14 / Rrt14


Mass: 23898.289 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: P40470
#74: Protein Exosome complex protein LRP1 / / Like an rRNA processing protein 1 / Yeast C1D domain-containing protein / rRNA processing protein 47


Mass: 21086.297 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: P38801
#75: Protein ATP-dependent RNA helicase DOB1 / mRNA transport regulator MTR4


Mass: 122228.031 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: P47047, RNA helicase
#76: Protein M-phase phosphoprotein 6 homolog / Exosome-associated RNA-binding protein MPP6


Mass: 21185.549 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: P53725

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

#21: 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
#22: 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

#23: 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
#50: 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

#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#39: 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
#40: 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
#41: 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
#49: 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
#56: 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
#57: 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 ... , 2 types, 2 molecules 5F5G

#42: 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
#43: 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

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

#46: 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
#47: 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

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

#54: 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
#55: 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

+
Unassigned helices ... , 2 types, 2 molecules X1X2

#61: Protein Unassigned helices 1


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
#62: Protein Unassigned helices 2


Mass: 59080.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c

+
Exosome complex component ... , 9 types, 9 molecules R5R1R3R6R2M3R0r4C4

#63: Protein Exosome complex component RRP45 / / Ribosomal RNA-processing protein 45


Mass: 34001.859 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: Q05636
#64: Protein Exosome complex component SKI6 / / Extracellular mutant protein 20 / Ribosomal RNA-processing protein 41 / Superkiller protein 6


Mass: 27599.727 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: P46948
#65: Protein Exosome complex component RRP43 / / Ribosomal RNA-processing protein 43


Mass: 44060.934 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: P25359
#66: Protein Exosome complex component RRP46 / / Ribosomal RNA-processing protein 46


Mass: 24430.193 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: P53256
#67: Protein Exosome complex component RRP42 / / Ribosomal RNA-processing protein 42


Mass: 29085.174 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: Q12277
#68: Protein Exosome complex component MTR3 / / mRNA transport regulator 3


Mass: 27603.988 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: P48240
#69: Protein Exosome complex component RRP40 / / Ribosomal RNA-processing protein 40


Mass: 26583.354 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: Q08285
#70: Protein Exosome complex component RRP4 / / Ribosomal RNA-processing protein 4


Mass: 39470.176 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: P38792
#71: Protein Exosome complex component CSL4 / / CEP1 synthetic lethal protein 4


Mass: 31619.279 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: P53859

+
Exosome complex exonuclease ... , 2 types, 2 molecules R4r6

#72: Protein Exosome complex exonuclease DIS3 / Chromosome disjunction protein 3 / Ribosomal RNA-processing protein 44


Mass: 113857.734 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: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#73: Protein Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 84160.570 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: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

+
Non-polymers , 3 types, 4 molecules

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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#78: 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
#79: 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 (Dhr1-depleted, state D) / Type: COMPLEX / Entity ID: #1-#76 / 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 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 10 / Num. of real images: 18028
Image scansMovie frames/image: 32 / Used frames/image: 1-32

-
Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1.8CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11RELIONinitial Euler assignment
12RELIONfinal Euler assignment
13RELIONclassification
14RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 382298
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75404 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6LQP

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more