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- PDB-7aju: Cryo-EM structure of the 90S-exosome super-complex (state Post-A1... -

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Open data

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Basic information

Entry

Database: PDB / ID: 7aju

Title

Cryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome)

Components

(40S ribosomal protein ...) x 18
(Exosome complex component ...) x 9
(Nucleolar complex protein ...) x 2
(Nucleolar protein ...) x 2
(Ribosomal RNA-processing protein ...) x 2
(U3 small nucleolar RNA-associated protein ...) x 17
(U3 small nucleolar ribonucleoprotein protein ...) x 2
(rRNA-processing protein ...) x 2
13 kDa ribonucleoprotein-associated protein
18S rRNA
5'ETS RNA
ATP-dependent RNA helicase DOB1
Bud site selection protein 21
Dimethyladenosine transferase
Essential nuclear protein 1
Exosome complex exonuclease DIS3
NET1-associated nuclear protein 1
Periodic tryptophan protein 2
Pre-rRNA-processing protein PNO1
Probable ATP-dependent RNA helicase DHR1
Protein SOF1
RNA
RNA 3'-terminal phosphate cyclase-like protein
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

Keywords

RIBOSOME / Ribosome biogenesis / Exosome / 90S pre-ribosome / A1 cleavage / Mtr4

Function / homology

Function and homology information

18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / CUT catabolic process ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / CUT catabolic process / regulation of ribosomal protein gene transcription by RNA polymerase II / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / box H/ACA snoRNA binding / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / exosome (RNase complex) / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / nuclear-transcribed mRNA catabolic process, non-stop decay / rRNA 2'-O-methylation / Noc4p-Nop14p complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / t-UTP complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear exosome (RNase complex) / Pwp2p-containing subcomplex of 90S preribosome / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / snoRNA guided rRNA 2'-O-methylation / rRNA modification / histone H2AQ104 methyltransferase activity / septum digestion after cytokinesis / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity / 3'-5' RNA helicase activity / tRNA re-export from nucleus / snRNA binding / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / nuclear mRNA surveillance / rRNA catabolic process / rRNA methyltransferase activity / rDNA heterochromatin / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / poly(A) binding / single-stranded telomeric DNA binding / mRNA 3'-UTR AU-rich region binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / O-methyltransferase activity / U4 snRNA binding / SUMOylation of RNA binding proteins / protein localization to nucleolus / 90S preribosome assembly / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / mTORC1-mediated signalling / rRNA methylation / Protein hydroxylation / U4 snRNP / poly(U) RNA binding / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / maturation of 5.8S rRNA / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / poly(A)+ mRNA export from nucleus / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / precatalytic spliceosome / preribosome, small subunit precursor / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / establishment of cell polarity / mRNA catabolic process / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / nucleolar large rRNA transcription by RNA polymerase I
Similarity search - Function

: / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / PIN domain / Exosome complex component RRP45 / Rrp40, S1 domain / : ...: / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / PIN domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / rRNA biogenesis protein Rrp5 / : / : / : / rRNA-processing arch domain / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Mtr4-like, beta-barrel domain / U3 small nucleolar RNA-associated protein 8 / : / Utp8, N-terminal beta propeller / Utp8, C-terminal / : / Ribonuclease II/R / RNB domain / RNB / : / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / U3 snoRNA associated / U3 snoRNA associated / Sof1-like protein / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20, C-terminal / : / : / : / Sof1-like domain / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20 domain / Small subunit processome component 20 homolog, C-terminal / WD repeat-containing protein 75 second beta-propeller / NOL6/Upt22 / BING4, C-terminal domain / Nucleolar complex protein 4 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / WD repeat-containing protein WDR46/Utp7 / Nrap protein domain 1 / BING4CT (NUC141) domain / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / BING4CT (NUC141) domain / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / : / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 4 / Small-subunit processome, Utp11 / Nucleolar protein 14 / Fcf2 pre-rRNA processing, C-terminal / Fcf2/DNTTIP2 / : / Utp11 protein / Nop14-like family / Fcf2 pre-rRNA processing / : / U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / rRNA-processing protein Fcf1, PIN domain / WDR3 second beta-propeller domain
Similarity search - Domain/homology

GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein uS8A ...GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / rRNA 2'-O-methyltransferase fibrillarin / Exosome complex component RRP43 / Ribosomal RNA-processing protein 7 / Periodic tryptophan protein 2 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / U3 small nucleolar ribonucleoprotein protein IMP3 / Small ribosomal subunit protein eS1A / Protein SOF1 / U3 small nucleolar RNA-associated protein 11 / U3 small nucleolar RNA-associated protein 20 / Small ribosomal subunit protein eS27A / Essential nuclear protein 1 / Exosome complex component RRP4 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar RNA-associated protein 18 / Dimethyladenosine transferase / U3 small nucleolar RNA-associated protein 10 / Exosome complex component SKI6 / ATP-dependent RNA helicase DOB1 / U3 small nucleolar RNA-associated protein MPP10 / Exosome complex component MTR3 / U3 small nucleolar RNA-associated protein 22 / Exosome complex component RRP46 / U3 small nucleolar RNA-associated protein 8 / 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 / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 14 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 / Exosome complex component RRP45 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 4 / rRNA processing protein RCL1 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / U3 small nucleolar RNA-associated protein 16 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 / Exosome complex component RRP42 / Nucleolar protein 56 / Nucleolar protein 58 / Small ribosomal subunit protein eS28A / Nucleolar complex protein 14 / Pre-rRNA-processing protein PNO1
Similarity search - Component

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Saccharomyces cerevisiae S288C (yeast)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å

Authors

Cheng, J. / Lau, B. / Flemming, D. / Venuta, G.L. / Berninghausen, O. / Beckmann, R. / Hurt, E.

Citation

Journal: Mol Cell / Year: 2021
Title: Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome.
Authors: Benjamin Lau / Jingdong Cheng / Dirk Flemming / Giuseppe La Venuta / Otto Berninghausen / Roland Beckmann / Ed Hurt /

Abstract: Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in ...

History

Deposition	Sep 29, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 3, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2	May 1, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Movie	Deposited structure unit Imaged by Jmol Download Superimposition on EM map EMDB-11808 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	7aju.cif.gz	5.6 MB	Display	PDBx/mmCIF format
PDB format	pdb7aju.ent.gz		Display	PDB format
PDBx/mmJSON format	7aju.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7aju_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	7aju_full_validation.pdf.gz	2.5 MB	Display
Data in XML	7aju_validation.xml.gz	717.4 KB	Display
Data in CIF	7aju_validation.cif.gz	1.1 MB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aj/7aju ftp://data.pdbj.org/pub/pdb/validation_reports/aj/7aju	HTTPS FTP

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Related structure data

Related structure data	11808MC 11807C 11809C 7ajtC M: map data used to model this data C: citing same article (ref.)
Similar structure data	11807 7ajt-d 11808 11809 4310 4308 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#161 - May 2013 Ricin similarity (98) #121 - Jan 2010 70S Ribosomes similarity (8) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (3) #253 - Jan 2021 Expressome similarity (7) #260 - Aug 2021 Ribonuclease P similarity (8) #10 - Oct 2000 Ribosome similarity (9) #86 - Feb 2007 Exosomes similarity (19) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #245 - May 2020 Spliceosomes similarity (8) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (3) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (7) #266 - Feb 2022 Oligosaccharyltransferase similarity (6) #227 - Nov 2018 Telomerase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #85 - Jan 2007 Importins similarity (2) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (4) #177 - Sep 2014 Apoptosomes similarity (2) #3 - Mar 2000 DNA Polymerase similarity (1) #166 - Oct 2013 Proteasome similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (3) #150 - Jun 2012 Sliding Clamps similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Assembly

Deposited unit

CA: rRNA 2'-O-methyltransferase fibrillarin

DA: 40S ribosomal protein S1-A

UA: Periodic tryptophan protein 2

CB: rRNA 2'-O-methyltransferase fibrillarin

UB: Nucleolar complex protein 14

UC: Something about silencing protein 10

UD: U3 small nucleolar RNA-associated protein 4

UE: U3 small nucleolar RNA-associated protein 5

UF: U3 small nucleolar RNA-associated protein 6

UG: U3 small nucleolar RNA-associated protein 7

UH: U3 small nucleolar RNA-associated protein 8

UI: U3 small nucleolar RNA-associated protein 9

UJ: U3 small nucleolar RNA-associated protein 10

UK: U3 small nucleolar RNA-associated protein 11

UL: U3 small nucleolar RNA-associated protein 12

UM: U3 small nucleolar RNA-associated protein 13

UN: U3 small nucleolar RNA-associated protein 14

UO: U3 small nucleolar RNA-associated protein 15

UP: Bud site selection protein 21

UQ: NET1-associated nuclear protein 1

UR: U3 small nucleolar RNA-associated protein 18

US: Nucleolar complex protein 4

UT: U3 small nucleolar RNA-associated protein 20

UU: U3 small nucleolar RNA-associated protein 21

UV: U3 small nucleolar RNA-associated protein 22

UX: rRNA-processing protein FCF1

CD: Nucleolar protein 56

CE: Nucleolar protein 58

CF: 13 kDa ribonucleoprotein-associated protein

CG: 13 kDa ribonucleoprotein-associated protein

CH: Ribosomal RNA-processing protein 9

CI: U3 small nucleolar ribonucleoprotein protein IMP3

CJ: U3 small nucleolar ribonucleoprotein protein IMP4

CK: U3 small nucleolar RNA-associated protein MPP10

CL: Ribosome biogenesis protein BMS1

CM: RNA 3'-terminal phosphate cyclase-like protein

CN: Ribosomal RNA-processing protein 7

JD: Probable ATP-dependent RNA helicase DHR1

JF: Ribosomal RNA small subunit methyltransferase NEP1

JG: Ribosomal RNA small subunit methyltransferase NEP1

JH: Essential nuclear protein 1

JI: rRNA biogenesis protein RRP5

JL: Dimethyladenosine transferase

JM: rRNA-processing protein FCF2

JP: Protein SOF1

Db: 40S ribosomal protein S27-A

JJ: Pre-rRNA-processing protein PNO1

DE: 40S ribosomal protein S4-A

DF: 40S ribosomal protein S5

DG: 40S ribosomal protein S6-A

DH: 40S ribosomal protein S7-A

DI: 40S ribosomal protein S8-A

DJ: 40S ribosomal protein S9-A

DL: 40S ribosomal protein S11-A

DN: 40S ribosomal protein S13

DO: 40S ribosomal protein S14-A

DQ: 40S ribosomal protein S16-A

DS: 40S ribosomal protein S18-A

DT: 40S ribosomal protein S19-A

DW: 40S ribosomal protein S22-A

DX: 40S ribosomal protein S23-A

DY: 40S ribosomal protein S24-A

Dc: 40S ribosomal protein S28-A

D2: 5'ETS RNA

D3: 18S rRNA

D4: U3 snoRNA

EA: RNA

EB: Exosome complex component RRP45

EC: Exosome complex component SKI6

ED: Exosome complex component RRP43

EE: Exosome complex component RRP46

EF: Exosome complex component RRP42

EG: Exosome complex component MTR3

EH: Exosome complex component RRP40

EI: Exosome complex component RRP4

EJ: Exosome complex component CSL4

EK: Exosome complex exonuclease DIS3

EN: ATP-dependent RNA helicase DOB1

hetero molecules

4.88 MDa, 78 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author
Evidence: microscopy

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Components

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Protein , 17 types, 20 molecules CACBUAUCUPUQCFCGCLCMJDJFJGJHJIJLJPJJEKEN

#1: Protein	rRNA 2'-O-methyltransferase fibrillarin / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA- ...Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA-associated protein NOP1 Mass: 34525.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Protein	Periodic tryptophan protein 2 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1 Mass: 104097.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P25635
#5: Protein	Something about silencing protein 10 / U three protein 3 / U3 small nucleolar RNA-associated protein 3 / U3 snoRNA-associated protein 11 Mass: 70364.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12136
#18: Protein	Bud site selection protein 21 / U three protein 16 / U3 small nucleolar RNA-associated protein 16 / U3 snoRNA-associated protein 16 Mass: 24431.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q08492
#19: Protein	NET1-associated nuclear protein 1 / U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar RNA- ...U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar RNA-associated protein 17 / U3 snoRNA-associated protein 17 Mass: 101341.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q02931
#28: Protein	13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein 1 Mass: 13582.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P39990
#33: Protein	Ribosome biogenesis protein 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
#34: Protein	RNA 3'-terminal phosphate cyclase-like protein Mass: 40220.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q08096
#36: Protein	Probable ATP-dependent RNA helicase DHR1 / DEAH box RNA helicase DHR1 / Extracellular mutant protein 16 Mass: 145171.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q04217, RNA helicase
#37: Protein	Ribosomal RNA small subunit methyltransferase NEP1 / 18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / ...18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / Essential for mitotic growth protein 1 / Nucleolar essential protein 1 Mass: 27936.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#38: Protein	Essential nuclear protein 1 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
#39: 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
#40: Protein	Dimethyladenosine transferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / 18S rRNA dimethylase / S- ...18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / 18S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase Mass: 36003.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P41819, 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
#42: Protein	Protein SOF1 / U3 small nucleolar RNA-associated protein SOF1 / U3 snoRNA-associated protein SOF1 Mass: 56888.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P33750
#44: Protein	Pre-rRNA-processing protein PNO1 / Partner of NOB1 / Ribosomal RNA-processing protein 20 Mass: 30380.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q99216
#74: 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
#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

+
40S ribosomal protein ... , 18 types, 18 molecules DADbDEDFDGDHDIDJDLDNDODQDSDTDWDXDYDc

#2: Protein	40S ribosomal protein S1-A / RP10A / Small ribosomal subunit protein eS1-A 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
#43: Protein	40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20 Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P35997
#45: Protein	40S ribosomal protein S4-A / RP5 / S7 / Small ribosomal subunit protein eS4-A / 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
#46: Protein	40S ribosomal protein S5 / RP14 / S2 / Small ribosomal subunit protein uS7 / 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
#47: Protein	40S ribosomal protein S6-A / RP9 / S10 / Small ribosomal subunit protein eS6-A / 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
#48: Protein	40S ribosomal protein S7-A / RP30 / RP40 / Small ribosomal subunit protein eS7-A Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P26786
#49: Protein	40S ribosomal protein S8-A / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9 Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#50: Protein	40S ribosomal protein S9-A / RP21 / S13 / Small ribosomal subunit protein uS4-A / 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
#51: Protein	40S ribosomal protein S11-A / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12 Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#52: Protein	40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15 Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05756
#53: Protein	40S ribosomal protein S14-A / RP59A / Small ribosomal subunit protein uS11-A Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P06367
#54: Protein	40S ribosomal protein S16-A / RP61R / Small ribosomal subunit protein uS9-A 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
#55: Protein	40S ribosomal protein S18-A / Small ribosomal subunit protein uS13-A Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX55
#56: Protein	40S ribosomal protein S19-A / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P07280
#57: Protein	40S ribosomal protein S22-A / RP50 / S24 / Small ribosomal subunit protein uS8-A / 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: P0C0W1
#58: Protein	40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / 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
#59: Protein	40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A 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
#60: Protein	40S ribosomal protein S28-A / S33 / Small ribosomal subunit protein eS28-A / YS27 Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9

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

#4: Protein	Nucleolar complex protein 14 / U three protein 2 / U3 small nucleolar RNA-associated protein 2 / U3 snoRNA-associated protein 2 Mass: 94463.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q99207
#21: Protein	Nucleolar complex protein 4 / U three protein 19 / U3 small nucleolar RNA-associated protein 19 / U3 snoRNA-associated protein 19 Mass: 63707.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q06512

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

#6: Protein	U3 small nucleolar RNA-associated protein 4 / U3 snoRNA-associated protein 4 / U three protein 4 / U3 protein 4 required for transcription / t-UTP4 Mass: 87909.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q06679
#7: Protein	U3 small nucleolar RNA-associated protein 5 / U3 snoRNA-associated protein 5 / U three protein 5 / U3 protein 5 required for transcription / t-UTP5 Mass: 72079.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q04177
#8: Protein	U3 small nucleolar RNA-associated protein 6 / U3 snoRNA-associated protein 6 / U three protein 6 Mass: 52495.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q02354
#9: Protein	U3 small nucleolar RNA-associated protein 7 / U3 snoRNA-associated protein 7 / U three protein 7 Mass: 62418.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P40055
#10: Protein	U3 small nucleolar RNA-associated protein 8 / U3 snoRNA-associated protein 8 / U three protein 8 / U3 protein 8 required for transcription / t-UTP8 Mass: 80269.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P53276
#11: Protein	U3 small nucleolar RNA-associated protein 9 / U3 snoRNA-associated protein 9 / U three protein 9 / U3 protein 9 required for transcription / t-UTP9 Mass: 65347.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38882
#12: Protein	U3 small nucleolar RNA-associated protein 10 / U3 snoRNA-associated protein 10 / U three protein 10 / U3 protein 10 required for transcription / t-UTP10 Mass: 200298.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P42945
#13: Protein	U3 small nucleolar RNA-associated protein 11 / U3 snoRNA-associated protein 11 / U three protein 11 Mass: 29806.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P34247
#14: Protein	U3 small nucleolar RNA-associated protein 12 / U3 snoRNA-associated protein 12 / DOM34-interacting protein 2 / U three protein 12 Mass: 106481.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12220
#15: Protein	U3 small nucleolar RNA-associated protein 13 / U3 snoRNA-associated protein 13 / U three protein 13 Mass: 91132.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q05946
#16: Protein	U3 small nucleolar RNA-associated protein 14 / U3 snoRNA-associated protein 14 / U three protein 14 Mass: 103189.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q04500
#17: Protein	U3 small nucleolar RNA-associated protein 15 / U3 snoRNA-associated protein 15 / U three protein 15 / U3 protein 15 required for transcription / t-UTP15 Mass: 57765.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q04305
#20: Protein	U3 small nucleolar RNA-associated protein 18 / U3 snoRNA-associated protein 18 / U three protein 18 Mass: 66494.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P40362
#22: 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
#23: Protein	U3 small nucleolar RNA-associated protein 21 / U3 snoRNA-associated protein 21 / U three protein 21 Mass: 104927.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q06078
#24: Protein	U3 small nucleolar RNA-associated protein 22 / U3 snoRNA-associated protein 22 / U three protein 22 Mass: 140660.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P53254
#32: Protein	U3 small nucleolar RNA-associated protein MPP10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10 Mass: 67042.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P47083

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

#25: Protein	rRNA-processing protein FCF1 / FAF1-copurifying factor 1 Mass: 21650.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q05498
#41: 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

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

#26: Protein	Nucleolar protein 56 / Ribosome biosynthesis protein SIK1 / Suppressor of I kappa b protein 1 Mass: 56961.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12460
#27: Protein	Nucleolar protein 58 / Nucleolar protein 5 Mass: 57060.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12499

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

#29: Protein	Ribosomal RNA-processing protein 9 Mass: 65146.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q06506
#35: Protein	Ribosomal RNA-processing protein 7 Mass: 34526.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P25368

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U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules CICJ

#30: Protein	U3 small nucleolar ribonucleoprotein protein IMP3 / U3 snoRNP protein IMP3 / Interacting with MPP10 protein 3 Mass: 21928.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32899
#31: Protein	U3 small nucleolar ribonucleoprotein protein IMP4 / U3 snoRNP protein IMP4 / Interacting with MPP10 protein 4 Mass: 33536.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P53941

+
RNA chain , 4 types, 4 molecules D2D3D4EA

#61: RNA chain	5'ETS RNA Mass: 26247.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#62: RNA chain	18S rRNA Mass: 580420.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#63: 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)
#64: RNA chain	RNA Mass: 6851.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)

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Exosome complex component ... , 9 types, 9 molecules EBECEDEEEFEGEHEIEJ

#65: 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
#66: 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
#67: 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
#68: 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
#69: 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
#70: 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
#71: 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
#72: 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
#73: 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

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Non-polymers , 3 types, 6 molecules

#76: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#77: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#78: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

+
Details

Has ligand of interest	N

-
Experimental details

-
Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component	Name: 90S-exosome super-complex in state Post-A1-exosome / Type: RIBOSOME / Entity ID: #1-#75 / Source: NATURAL
Source (natural)	Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solution	pH: 7.4
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD
Image recording	Electron dose: 44 e/Å² / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software	Name: CTFFIND / Category: CTF correction
CTF correction	Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction	Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35320 / Symmetry type: POINT
Atomic model building	Protocol: RIGID BODY FIT
Atomic model building	PDB-ID: 6ZQD 6zqd Accession code: 6ZQD / Source name: PDB / Type: experimental model

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+Protein , 17 types, 20 molecules CACBUAUCUPUQCFCGCLCMJDJFJGJHJIJLJPJJEKEN

+40S ribosomal protein ... , 18 types, 18 molecules DADbDEDFDGDHDIDJDLDNDODQDSDTDWDXDYDc

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

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

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

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

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

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

+RNA chain , 4 types, 4 molecules D2D3D4EA

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

+Non-polymers , 3 types, 6 molecules

+Details

-Experimental details

-Experiment

-Sample preparation

-Electron microscopy imaging

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

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