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- PDB-6zqf: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -

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Basic information

Entry
Database: PDB / ID: 6zqf
TitleCryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-B (Poly-Ala)
Components
  • (40S ribosomal protein ...) x 18
  • (Nucleolar complex protein ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 5
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • 18S rRNA18S ribosomal RNA
  • 5ETS RNA
  • Dimethyladenosine transferase
  • Essential nuclear protein 1
  • Periodic tryptophan protein 2
  • Pre-rRNA-processing protein PNO1
  • Probable ATP-dependent RNA helicase DHR1
  • RNA 3'-terminal phosphate cyclase-like protein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Ribosomal RNA-processing protein 7
  • Ribosome biogenesis protein BMS1
  • Rps5p
  • Something about silencing protein 10
  • U3 snoRNA
KeywordsRIBOSOME / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1
Function / homology
Function and homology information


18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / Noc4p-Nop14p complex / CURI complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA small subunit pseudouridine methyltransferase Nep1 / Mpp10 complex / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA (pseudouridine) methyltransferase activity ...18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / Noc4p-Nop14p complex / CURI complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA small subunit pseudouridine methyltransferase Nep1 / Mpp10 complex / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA (pseudouridine) methyltransferase activity / septum digestion after cytokinesis / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / rRNA base methylation / single-stranded telomeric DNA binding / sno(s)RNA-containing ribonucleoprotein complex / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / tRNA export from nucleus / 90S preribosome / preribosome, small subunit precursor / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA 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 / small-subunit processome / ribosomal small subunit biogenesis / proteasome assembly / nuclear periphery / establishment of cell polarity / endoribonuclease activity / maintenance of translational fidelity / positive regulation of translational fidelity / enzyme activator activity / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / rRNA processing / cytoplasmic translation / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / ribosome / rRNA binding / RNA helicase / structural constituent of ribosome / mitochondrial matrix / cell cycle / translation / RNA helicase activity / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Nrap protein domain 6 / Nrap protein, domain 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...Nrap protein domain 6 / Nrap protein, domain 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / S-adenosyl-L-methionine-dependent methyltransferase / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Nrap protein domain 1 / Nrap protein, domain 3 / Anaphase-promoting complex subunit 4, WD40 domain / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Periodic tryptophan protein 2 / Ribosomal RNA-processing protein 7, C-terminal domain / in:ipr038111: / Ribosomal protein S3Ae, conserved site / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S7 domain / Ribosomal protein S8e, conserved site / Sas10 C-terminal domain / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal protein S7, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / RNA 3'-terminal phosphate cyclase domain / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S4e, central region / Krr1 KH1 domain / Ribosomal protein S19e / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S24e / S25 ribosomal protein / Ribosomal protein S27 / Ribosomal protein S28e / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / Helicase associated domain (HA2) / Oligonucleotide/oligosaccharide-binding (OB)-fold / EMG1/NEP1 methyltransferase / Bystin / Ribosomal RNA adenine dimethylase / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Dip2/Utp12 Family / Nop14-like family / Sas10/Utp3/C1D family / Sas10 C-terminal domain / Utp13 specific WD40 associated domain / CBF/Mak21 family / Utp21 specific WD40 associated putative domain / Nrap protein domain 1 / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosome biogenesis protein Bms1/Tsr1 / RNA 3'-terminal phosphate cyclase / Pre-rRNA-processing protein PNO1-like
40S ribosomal protein S8-A / 40S ribosomal protein S9-A / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 13 / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein MPP10 / Dimethyladenosine transferase / 40S ribosomal protein S27-A ...40S ribosomal protein S8-A / 40S ribosomal protein S9-A / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 13 / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein MPP10 / Dimethyladenosine transferase / 40S ribosomal protein S27-A / Ribosomal RNA small subunit methyltransferase NEP1 / 40S ribosomal protein S1-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S7-A / 40S ribosomal protein S5 / Periodic tryptophan protein 2 / Ribosomal RNA-processing protein 7 / 40S ribosomal protein S18-A / U3 small nucleolar RNA-associated protein 21 / Nucleolar complex protein 4 / 40S ribosomal protein S16-A / 40S ribosomal protein S4-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S19-A / 40S ribosomal protein S22-A / 40S ribosomal protein S23-A / 40S ribosomal protein S24-A / 40S ribosomal protein S6-A / RNA 3'-terminal phosphate cyclase-like protein / Pre-rRNA-processing protein PNO1 / Nucleolar complex protein 14 / 40S ribosomal protein S28-A / 40S ribosomal protein S25-A / U3 small nucleolar RNA-associated protein 12 / Something about silencing protein 10 / Ribosome biogenesis protein BMS1 / 40S ribosomal protein S11-A
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsCheng, J. / Lau, B. / Venuta, G.L. / Berninghausen, O. / Hurt, E. / Beckmann, R.
CitationJournal: Science / Year: 2020
Title: 90 pre-ribosome transformation into the primordial 40 subunit.
Authors: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann /
Abstract: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
UA: Periodic tryptophan protein 2
UB: Nucleolar complex protein 14
UC: Something about silencing protein 10
UL: U3 small nucleolar RNA-associated protein 12
UM: U3 small nucleolar RNA-associated protein 13
US: Nucleolar complex protein 4
UU: U3 small nucleolar RNA-associated protein 21
UV: U3 small nucleolar RNA-associated protein 22
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
JL: Dimethyladenosine transferase
JJ: Pre-rRNA-processing protein PNO1
DF: Rps5p
DQ: 40S ribosomal protein S16-A
DS: 40S ribosomal protein S18-A
DT: 40S ribosomal protein S19-A
Dc: 40S ribosomal protein S28-A
D2: 5ETS RNA
D3: 18S rRNA
DA: 40S ribosomal protein S1-A
DE: 40S ribosomal protein S4-A
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
DZ: 40S ribosomal protein S25-A
DW: 40S ribosomal protein S22-A
DX: 40S ribosomal protein S23-A
DY: 40S ribosomal protein S24-A
Db: 40S ribosomal protein S27-A
D4: U3 snoRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,365,30643
Polymers2,365,24042
Non-polymers651
Water0
1


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

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Components

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Protein , 11 types, 12 molecules UAUCCLCMCNJDJFJGJHJLJJDF

#1: 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
#3: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: Protein Rps5p


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

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

#2: 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
#6: 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

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U3 small nucleolar RNA-associated protein ... , 5 types, 5 molecules ULUMUUUVCK

#4: 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
#5: 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
#7: 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
#8: 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
#11: 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

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

#9: 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
#10: 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

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

#21: Protein 40S ribosomal protein S16-A / Ribosome / 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
#22: Protein 40S ribosomal protein S18-A / Ribosome / 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
#23: Protein 40S ribosomal protein S19-A / Ribosome / 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
#24: Protein 40S ribosomal protein S28-A / Ribosome / 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
#27: Protein 40S ribosomal protein S1-A / Ribosome / 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
#28: Protein 40S ribosomal protein S4-A / Ribosome / 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
#29: Protein 40S ribosomal protein S6-A / Ribosome / 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
#30: Protein 40S ribosomal protein S7-A / Ribosome / 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
#31: Protein 40S ribosomal protein S8-A / Ribosome / 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
#32: Protein 40S ribosomal protein S9-A / Ribosome / 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
#33: Protein 40S ribosomal protein S11-A / Ribosome / 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
#34: 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
#35: Protein 40S ribosomal protein S14-A / Ribosome / 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
#36: Protein 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


Mass: 12067.272 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: Q3E792
#37: Protein 40S ribosomal protein S22-A / Ribosome / 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
#38: Protein 40S ribosomal protein S23-A / Ribosome / 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
#39: Protein 40S ribosomal protein S24-A / Ribosome / 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
#40: Protein 40S ribosomal protein S27-A / Ribosome / 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

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RNA chain , 3 types, 3 molecules D2D3D4

#25: RNA chain 5ETS RNA


Mass: 6441.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#26: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 566062.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#41: RNA chain U3 snoRNA


Mass: 11187.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)

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Non-polymers , 1 types, 1 molecules

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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 90S pre-ribbosome state Dis-B / Type: RIBOSOME / Entity ID: #1-#41 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: accharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16654 / Symmetry type: POINT

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