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

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Open data

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Basic information

Entry

Database: PDB / ID: 6zqa

Title

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala)

Components

(40S ribosomal protein ...) x 11
(Nucleolar complex protein ...) x 2
(Nucleolar protein ...Nucleolus) x 2
(Ribosomal RNA-processing protein ...) x 2
(Ribosome biogenesis protein ...) x 2
(U3 small nucleolar RNA-associated protein ...) x 16
(U3 small nucleolar ribonucleoprotein protein ...) x 2
(rRNA-processing protein ...) x 2
13 kDa ribonucleoprotein-associated protein
18S rRNA18S ribosomal RNA
5ETS RNA
Bud site selection protein 21
Essential nuclear protein 1
KRR1 small subunit processome component
NET1-associated nuclear protein 1
Periodic tryptophan protein 2
Pre-rRNA-processing protein PNO1
Protein FAF1
Protein SOF1
RNA 3'-terminal phosphate cyclase-like protein
Regulator of rDNA transcription protein 14
Ribosomal RNA small subunit methyltransferase NEP1
Rps5p
Something about silencing protein 10
U3 snoRNA
rRNA 2'-O-methyltransferase fibrillarin

Keywords

RIBOSOME / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage /

Dhr1

Function / homology

Function and homology information

Noc4p-Nop14p complex /

regulation of ribosomal protein gene transcription by RNA polymerase II /

rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / septum digestion after cytokinesis /

snRNA binding / positive regulation of RNA binding / SUMOylation of RNA binding proteins / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / 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) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / rRNA methyltransferase activity / positive regulation of rRNA processing / box C/D methylation guide snoRNP complex / rRNA base methylation / single-stranded telomeric DNA binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex /

U4 snRNA binding / protein localization to nucleolus /

O-methyltransferase activity /

Protein hydroxylation / rRNA methylation / U3 snoRNA binding / : / poly(A)+ mRNA export from nucleus / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / precatalytic spliceosome / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor /

snoRNA binding / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / nucleolar large rRNA transcription by RNA polymerase I / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression /

enzyme activator activity /

proteasome assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity /

RNA processing / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity /

Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / small-subunit processome / maintenance of translational fidelity /

ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding /

mRNA splicing, via spliceosome / rRNA processing /

ribosomal small subunit assembly / cytosolic small ribosomal subunit / unfolded protein binding /

ribosome biogenesis / small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit /

tRNA binding /

rRNA binding /

ribosome / structural constituent of ribosome /

cell cycle /

translation /

mRNA binding /

GTPase activity / GTP binding /

nucleolus /

ATP hydrolysis activity /

mitochondrion /

RNA binding /

nucleoplasm /

Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / U3 small nucleolar RNA-associated protein 8 / Utp8 family / : / : / : /

KRR1 small subunit processome component, second KH domain / Ribosomal RNA assembly KRR1 / U3 snoRNA associated ...Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / U3 small nucleolar RNA-associated protein 8 / Utp8 family / : / : / : /

KRR1 small subunit processome component, second KH domain / Ribosomal RNA assembly KRR1 / U3 snoRNA associated / Nucleolar complex protein 4 / U3 snoRNA associated /

Nucleolar protein 14 / Nop14-like family / U3 small nucleolar RNA-associated protein 6 / rRNA-processing protein Fcf1, PIN domain / U3 small nucleolar RNA-associated protein 6 / NOL6/Upt22 / Small-subunit processome, Utp11 / Sof1-like protein / BING4, C-terminal domain / Fcf2 pre-rRNA processing, C-terminal /

Nrap protein domain 1 /

Nrap protein, domain 2 /

Nrap protein, domain 3 /

Nrap protein, domain 4 /

Nrap protein, domain 5 /

Nrap protein, domain 6 / Ribosomal RNA-processing protein Rrp9-like / Fcf2/DNTTIP2 / WD repeat-containing protein WDR46/Utp7 /

Nrap protein domain 1 / Utp11 protein / Sof1-like domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing /

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 / rRNA-processing protein Fcf1/Utp23 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain /

Fcf1 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Small-subunit processome, Utp14 / U3 small nucleolar RNA-associated protein 15, C-terminal / Utp14 protein / UTP15 C terminal / Sas10 C-terminal domain / Sas10 C-terminal domain /

Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal /

Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / RNA 3'-terminal phosphate cyclase signature. / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Sas10/Utp3/C1D / Small-subunit processome, Utp21 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2 / Sas10/Utp3/C1D family / Mpp10 protein / Utp21 specific WD40 associated putative domain /

Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain /

Nucleolar protein Nop56/Nop58 / CCAAT-binding factor / CBF/Mak21 family /

Krr1, KH1 domain / Krr1 KH1 domain / Bystin / Bystin / rRNA 2'-O-methyltransferase fibrillarin-like /

Fibrillarin, conserved site /

Fibrillarin / Fibrillarin signature. /

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 uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 /

KRR1 small subunit processome component / 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 / Small ribosomal subunit protein eS27A /

Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar RNA-associated protein 18 / Regulator of rDNA transcription protein 14 / Protein FAF1 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 6 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 14 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 /

Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 4 / RNA 3'-terminal phosphate cyclase-like protein / Bud site selection protein 21 /

Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 /

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: 4.4 Å

Authors

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

Citation

Journal: 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 ...

History

Deposition	Jul 9, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 23, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2020	Group: 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

Movie	Deposited structure unit Imaged by Jmol Download Superimposition on EM map EMDB-11357 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	6zqa.cif.gz	3.5 MB	Display	PDBx/mmCIF format
PDB format	pdb6zqa.ent.gz		Display	PDB format
PDBx/mmJSON format	6zqa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zq/6zqa ftp://data.pdbj.org/pub/pdb/validation_reports/zq/6zqa	HTTPS FTP

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Related structure data

Related structure data	11357MC 11358C 11359C 11360C 11361C 11362C 11363C 6zqbC 6zqcC 6zqdC 6zqeC 6zqfC 6zqgC M: map data used to model this data C: citing same article (ref.)
Similar structure data	10176 5fl8-d 5oql-d 3769 21471 4316 11034 5ijo-d 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 (54) #121 - Jan 2010 70S Ribosomes similarity (11) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (6) #10 - Oct 2000 Ribosome similarity (9) #260 - Aug 2021 Ribonuclease P similarity (8) #253 - Jan 2021 Expressome similarity (3) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR 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) #87 - Mar 2007 Zinc Fingers similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action 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 (6) #266 - Feb 2022 Oligosaccharyltransferase similarity (6) #227 - Nov 2018 Telomerase similarity (2) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #104 - Aug 2008 Selenocysteine Synthase 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 (1) #177 - Sep 2014 Apoptosomes similarity (2) #3 - Mar 2000 DNA Polymerase similarity (1) #86 - Feb 2007 Exosomes similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Assembly

Deposited unit

UA: Periodic tryptophan protein 2

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

UU: U3 small nucleolar RNA-associated protein 21

UV: U3 small nucleolar RNA-associated protein 22

UX: rRNA-processing protein FCF1

UZ: Ribosome biogenesis protein UTP30

CA: rRNA 2'-O-methyltransferase fibrillarin

CB: rRNA 2'-O-methyltransferase fibrillarin

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

JF: Ribosomal RNA small subunit methyltransferase NEP1

JG: Ribosomal RNA small subunit methyltransferase NEP1

JH: Essential nuclear protein 1

JJ: Pre-rRNA-processing protein PNO1

JM: rRNA-processing protein FCF2

JN: Protein FAF1

JO: KRR1 small subunit processome component

JP: Protein SOF1

JQ: Regulator of rDNA transcription protein 14

DA: 40S ribosomal protein S1-A

DF: Rps5p

DH: 40S ribosomal protein S7-A

DJ: 40S ribosomal protein S9-A

DN: 40S ribosomal protein S13

DO: 40S ribosomal protein S14-A

DQ: 40S ribosomal protein S16-A

DS: 40S ribosomal protein S18-A

DW: 40S ribosomal protein S22-A

DX: 40S ribosomal protein S23-A

Db: 40S ribosomal protein S27-A

Dc: 40S ribosomal protein S28-A

D2: 5ETS RNA

D3: 18S rRNA

D4: U3 snoRNA

hetero molecules

3.7 MDa, 60 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 , 15 types, 18 molecules UAUCUPUQCACBCFCGCMJFJGJHJJJNJOJPJQDF

#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
#16: 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
#17: 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
#24: 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
#27: 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	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
#35: 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
#36: 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
#37: 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
#39: Protein	Protein FAF1 / Forty S assembly factor Mass: 38961.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P40546
#40: Protein	KRR1 small subunit processome component / / KRR-R motif-containing protein 1 / Ribosomal RNA assembly protein KRR1 Mass: 37226.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P25586
#41: 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
#42: Protein	Regulator of rDNA transcription protein 14 Mass: 23898.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P40470
#44: 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
#19: 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 ... , 16 types, 16 molecules UDUEUFUGUHUIUJUKULUMUNUOURUUUVCK

#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#18: 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
#20: 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
#21: 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
#31: 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

#22: 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
#38: 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

+
Ribosome biogenesis protein ... , 2 types, 2 molecules UZCL

#23: Protein	Ribosome biogenesis protein UTP30 / / U3 snoRNP-associated protein UTP30 Mass: 31668.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P36144
#32: 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

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

#25: Protein	Nucleolar protein 56 / Nucleolus / 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
#26: 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 CHCN

#28: 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
#34: 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

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

#29: 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
#30: 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

+
40S ribosomal protein ... , 11 types, 11 molecules DADHDJDNDODQDSDWDXDbDc

#43: 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
#45: 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
#46: 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
#47: 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
#48: 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
#49: 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
#50: 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
#51: 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
#52: 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
#53: 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
#54: 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

+
RNA chain , 3 types, 3 molecules D2D3D4

#55: RNA chain	5ETS RNA Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#56: RNA chain	18S rRNA / 18S ribosomal RNA Mass: 444436.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#57: RNA chain	U3 snoRNA Mass: 56132.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)

+
Non-polymers , 3 types, 5 molecules

#58: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#59: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#60: 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

+
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 pre-ribbosome state A / Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL
Molecular weight	Experimental value: NO
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
Specimen support	Grid material: COPPER / Grid type: Quantifoil
Vitrification	Cryogen name: ETHANE

-
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

Bright-field microscopy

Image recording

ID	Imaging-ID	Electron dose (e/Å²)	Film or detector model
1	1	44	GATAN K2 SUMMIT (4k x 4k)
2	1	44	GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correction	Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction	Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11194 / Symmetry type: POINT

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+Protein , 15 types, 18 molecules UAUCUPUQCACBCFCGCMJFJGJHJJJNJOJPJQDF

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

+U3 small nucleolar RNA-associated protein ... , 16 types, 16 molecules UDUEUFUGUHUIUJUKULUMUNUOURUUUVCK

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

+Ribosome biogenesis protein ... , 2 types, 2 molecules UZCL

+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

+40S ribosomal protein ... , 11 types, 11 molecules DADHDJDNDODQDSDWDXDbDc

+RNA chain , 3 types, 3 molecules D2D3D4

+Non-polymers , 3 types, 5 molecules

+Details

-Experimental details

-Experiment

-Sample preparation

-Electron microscopy imaging

-Processing

+About Yorodumi

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