EMDB-0951: Cryo-EM structure of 90S small subunit preribosomes in transition...

Basic information

• Entry: Database: EMDB / ID: EMD-0951
• Title: Cryo-EM structure of 90S small subunit preribosomes in transition states (State C)

Sample

90S pre-ribosome (Dhr1-depleted, state C)

• (nucleic-acidNucleic acid) x 3
• (40S ribosomal protein ...) x 16
• rRNA 2'-O-methyltransferase fibrillarin
• (Nucleolar protein ...Nucleolus) x 2
• (Ribosomal RNA-processing protein ...) x 2
• 13 kDa ribonucleoprotein-associated protein
• (U3 small nucleolar RNA-associated protein ...) x 17
• NET1-associated nuclear protein 1
• Periodic tryptophan protein 2
• Bud site selection protein 21
• (U3 small nucleolar ribonucleoprotein protein ...) x 3
• Something about silencing protein 10
• Protein SOF1
• (rRNA-processing protein ...) x 2
• (Ribosome biogenesis protein ...) x 2
• rRNA biogenesis protein RRP5
• Ribosomal RNA small subunit methyltransferase NEP1
• RNA 3'-terminal phosphate cyclase-like protein
• RNA cytidine acetyltransferase
• (Nucleolar complex protein ...) x 2
• Essential nuclear protein 1
• Pno1
• Protein BFR2
• Unassigned helices
• (ligand) x 3

Function / homology

Function:

rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / CURI complex / t-UTP complex / tRNA acetylation / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / mRNA modification / histone-glutamine methyltransferase activity / box C/D RNA binding / box C/D RNA 3'-end processing / Mpp10 complex / box H/ACA snoRNA binding / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / septum digestion after cytokinesis / rRNA modification / regulation of transcription by RNA polymerase I / 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) / positive regulation of RNA binding / rDNA heterochromatin / nuclear microtubule / 90S preribosome assembly / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / box C/D RNP complex / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / small nuclear ribonucleoprotein complex / protein localization to nucleolus / U4 snRNA binding / histone glutamine methylation / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / sno(s)RNA-containing ribonucleoprotein complex / tRNA export from nucleus / precatalytic spliceosome / 90S preribosome / preribosome, small subunit precursor / O-methyltransferase activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA binding / poly(U) RNA binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / vesicle-mediated transport / positive regulation of translational fidelity / maintenance of translational fidelity / enzyme activator activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / protein transport / ribosome biogenesis / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / cell cycle / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding

Domain/homology:

Ribosomal protein S13/S15, N-terminal / Apoptosis-antagonizing transcription factor, C-terminal / Small-subunit processome, Utp21 / Helicase domain / Bystin / S15/NS1, RNA-binding / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc-binding ribosomal protein / Down-regulated-in-metastasis protein / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Nucleic acid-binding, OB-fold / NUC153 / Nucleotide-binding alpha-beta plait domain superfamily / Nucleolar protein 14 / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / BING4, C-terminal domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / U3 snoRNA associated / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Sof1-like protein / Small-subunit processome, Utp12 / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S11 / Ribosomal protein S24e / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / Nop domain / PIN domain / RNA-binding S4 domain / S1 domain / HAT (Half-A-TPR) repeat / ATPase, AAA-type, core / Ribosomal protein L7Ae conserved site / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Sas10/Utp3/C1D / NOL6/Upt22 / CCAAT-binding factor / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / KOW / Ribosomal protein S12/S23 / Small-subunit processome, Utp14 / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp11 / Small-subunit processome, Utp13 / Ribosomal protein S6, eukaryotic / Nrap protein, domain 3 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S15P / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA-processing protein 7, C-terminal domain / Anaphase-promoting complex subunit 4, WD40 domain / AATF leucine zipper-containing domain / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / Ribosomal protein S28e conserved site / Ribosomal protein S4/S9 / Helix hairpin bin domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Nrap protein domain 1 / RNA-binding domain, S1 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S8e, conserved site / Ribosomal protein L2, domain 2 / Fcf2 pre-rRNA processing, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / 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 S3Ae, conserved site

Component:

Ribosomal RNA small subunit methyltransferase NEP1 / RNA cytidine acetyltransferase / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 6 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 14 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Nucleolar protein 58 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / Protein BFR2 / 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 / U3 small nucleolar RNA-associated protein 22 / 40S ribosomal protein S28-A / 40S ribosomal protein S22-B / U3 small nucleolar RNA-associated protein 8 / Protein SOF1 / Ribosome biogenesis protein ENP2 / Periodic tryptophan protein 2 / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S23-A / 40S ribosomal protein S24-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / 40S ribosomal protein S5 / U3 small nucleolar RNA-associated protein MPP10 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S1-A / U3 small nucleolar RNA-associated protein 11 / U3 small nucleolar RNA-associated protein 20 / 40S ribosomal protein S27-A / 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 ribonucleoprotein protein LCP5 / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / Nucleolar complex protein 14

• Biological species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast)
• Method: single particle reconstruction / cryo EM / Resolution: 8.6 Å
• Authors: Du Y / Ye K

Funding support

China, 2 items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	91940302, 91540201, 31430024, 31325007	China
Chinese Academy of Sciences	XDB08010203	China

• Citation: Journal: Science / Year: 2020; Title: Cryo-EM structure of 90 small ribosomal subunit precursors in transition states.; Authors: Yifei Du / Weidong An / Xing Zhu / Qi Sun / Jia Qi / Keqiong Ye / ; Abstract: The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of intermediates in the path from the 90 to the pre-40 The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 progression.
• Validation Report: Summary, Full report, XML, About validation report

History

Deposition	Jan 14, 2020	-
Header (metadata) release	Sep 16, 2020	-
Map release	Sep 16, 2020	-
Update	Sep 30, 2020	-
Current status	Sep 30, 2020	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_0951.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.334 Å

Density

Contour Level	By AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum	-0.022908993 - 0.06173087
Average (Standard dev.)	0.00047282316 (±0.0029305615)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 448 448 448 Spacing 448 448 448
Cell	A=B=C: 597.632 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.334	1.334	1.334
M x/y/z	448	448	448
origin x/y/z	0.000	0.000	0.000
length x/y/z	597.632	597.632	597.632
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	448	448	448
D min/max/mean	-0.023	0.062	0.000

Supplemental data

Sample components

Entire 90S pre-ribosome (Dhr1-depleted, state C)

• Entire: Name: 90S pre-ribosome (Dhr1-depleted, state C) / Number of components: 68

Component #1: protein, 90S pre-ribosome (Dhr1-depleted, state C)

• Protein: Name: 90S pre-ribosome (Dhr1-depleted, state C) / Recombinant expression: No
• Mass: Theoretical: 5 MDa
• Source: Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c

Component #2: nucleic-acid, U3 snoRNA

nucleic acid

Name: U3 snoRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

GUCGACGUAC UUCAUAGGAU CAUUUCUAUA GGAAUCGUCA CUCUUUGACU CUUCAAAAGA GCCACUGAAU CCAACUUGGU UGAUGAGUCC CAUAACCUUU GUACCCCAGA GUGAGAAACC GAAAUUGAAU CUAAAUUAGC UUGGUCCGCA AUCCUUAGCG GUUCGGCCAU CUAUAAUUUU GAAUAAAAAU UUUGCUUUGC CGUUGCAUUU GUAGUUUUUU CCUUUGGAAG UAAUUACAAU AUUUUAUGGC GCGAUGAUCU UGACCCAUCC UAUGUACUUC UUUUUUGAAG GGAUAGGGCU CUAUGGGUGG GUACAAAUGG CAGUCUGACA AGU

• Mass: Theoretical: 106.503258 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #3: nucleic-acid, 5' ETS

nucleic acid

Name: 5' ETS / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

AUGCGAAAGC AGUUGAAGAC AAGUUCGAAA AGAGUUUGGA AACGAAUUCG AGUAGGCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG CUAGGUGAUC GUCAGAUCUG CCUAGUCUCU AUACAGCGUG UUUAAUUGAC AUGGGUUGAU GCGUAUUGAG AGAUACAAUU UGGGAAGAAA UUCCCAGAGU GUGUUUCUUU UGCGUUUAAC CUGAACAGUC UCAUCGUGGG CAUCUUGCGA UUCCAUUGGU GAGCAGCGAA GGAUUUGGUG GAUUACUAGC UAAUAGCAAU CUAUUUCAAA GAAUUCAAAC UUGGGGGAAU GCCUUGUUGA AUAGCCGGUC GCAAGACUGU GAUUCUUCAA GUGUAACCUC CUCUCAAAUC AGCGAUAUCA AACGUACCAU UCCGUGAAAC ACCGGGGUAU CUGUUUGGUG GAACCUGAUU AGAGGAAACU CAAAGAGUGC UAUGGUAUGG UGACGGAGUG CGCUGGUCAA GAGUGUAAAA GCUUUUUGAA CAGAGAGCAU UUCCGGCAGC AGAGAGACCU GAAAAAGCAA UUUUUCUGGA AUUUCAGCUG UUUCCAAACU CAAUAAGUAU CUUCUAGCAA GAGGGAAUAG GUGGGAAAAA AAAAAAGAGA UUUCGGUUUC UUUCUUUUUU ACUGCUUGUU GCUUCUUCUU UUAAGAUAGU

• Mass: Theoretical: 225.543094 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #4: nucleic-acid, 18S pre-rRNA

nucleic acid

Name: 18S pre-rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

AAGAUAGUUA UCUGGUUGAU CCUGCCAGUA GUCAUAUGCU UGUCUCAAAG AUUAAGCCAU GCAUGUCUAA GUAUAAGCAA UUUAUACAGU GAAACUGCGA AUGGCUCAUU AAAUCAGUUA UCGUUUAUUU GAUAGUUCCU UUACUACAUG GUAUAACUGU GGUAAUUCUA GAGCUAAUAC AUGCUUAAAA UCUCGACCCU UUGGAAGAGA UGUAUUUAUU AGAUAAAAAA UCAAUGUCUU CGGACUCUUU GAUGAUUCAU AAUAACUUUU CGAAUCGCAU GGCCUUGUGC UGGCGAUGGU UCAUUCAAAU UUCUGCCCUA UCAACUUUCG AUGGUAGGAU AGUGGCCUAC CAUGGUUUCA ACGGGUAACG GGGAAUAAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCAAUCCUAA UUCAGGGAGG UAGUGACAAU AAAUAACGAU ACAGGGCCCA UUCGGGUCUU GUAAUUGGAA UGAGUACAAU GUAAAUACCU UAACGAGGAA CAAUUGGAGG GCAAGUCUGG UGCCAGCAGC CGCGGUAAUU CCAGCUCCAA UAGCGUAUAU UAAAGUUGUU GCAGUUAAAA AGCUCGUAGU UGAACUUUGG GCCCGGUUGG CCGGUCCGAU UUUUUCGUGU ACUGGAUUUC CAACGGGGCC UUUCCUUCUG GCUAACCUUG AGUCCUUGUG GCUCUUGGCG AACCAGGACU UUUACUUUGA AAAAAUUAGA GUGUUCAAAG CAGGCGUAUU GCUCGAAUAU AUUAGCAUGG AAUAAUAGAA UAGGACGUUU GGUUCUAUUU UGUUGGUUUC UAGGACCAUC GUAAUGAUUA AUAGGGACGG UCGGGGGCAU CAGUAUUCAA UUGUCAGAGG UGAAAUUCUU GGAUUUAUUG AAGACUAACU ACUGCGAAAG CAUUUGCCAA GGACGUUUUC AUUAAUCAAG AACGAAAGUU AGGGGAUCGA AGAUGAUCAG AUACCGUCGU AGUCUUAACC AUAAACUAUG CCGACUAGGG AUCGGGUGGU GUUUUUUUAA UGACCCACUC GGCACCUUAC GAGAAAUCAA AGUCUUUGGG UUCUGGGGGG AGUAUGGUCG CAAGGCUGAA ACUUAAAGGA AUUGACGGAA GGGCACCACC AGGAGUGGAG CCUGCGGCUU AAUUUGACUC AACACGGGGA AACUCACCAG GUCCAGACAC AAUAAGGAUU GACAGAUUGA GAGCUCUUUC UUGAUUUUGU GGGUGGUGGU GCAUGGCCGU UCUUAGUUGG UGGAGUGAUU UGUCUGCUUA AUUGCGAUAA CGAACGAGAC CUUAACCUAC UAAAUAGUGG UGCUAGCAUU UGCUGGUUAU CCACUUCUUA GAGGGACUAU CGGUUUCAAG CCGAUGGAAG UUUGAGGCAA UAACAGGUCU GUGAUGCCCU UAGACGUUCU GGGCCGCACG CGCGCUACAC UGACGGAGCC AGCGAGUCUA ACCUUGGCCG AGAGGUCUUG GUAAUCUUGU GAAACUCCGU CGUGCUGGGG AUAGAGCAUU GUAAUUAUUG CUCUUCAACG AGGAAUUCCU AGUAAGCGCA AGUCAUCAGC UUGCGUUGAU UACGUCCCUG CCCUUUGUAC ACACCGCCCG UCGCUAGUAC CGAUUGAAUG GCUUAGUGAG GCCUCAGGAU CUGCUUAGAG AAGGGGGCAA CUCCAUCUCA GAGCGGAGAA UUUGGACAAA CUUGGUCAUU UAGAGGAACU AAAAGUCGUA ACAAGGUUUC CGUAGGUGAA CCUGCGGAAG GAUCAUUAA

• Mass: Theoretical: 582.710875 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #5: protein, 40S ribosomal protein S1-A

• Protein: Name: 40S ribosomal protein S1-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 28.798467 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #6: protein, 40S ribosomal protein S4-A

• Protein: Name: 40S ribosomal protein S4-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 29.46933 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #7: protein, 40S ribosomal protein S5

• Protein: Name: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 25.0726 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #8: protein, 40S ribosomal protein S6-A

• Protein: Name: 40S ribosomal protein S6-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 27.054486 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #9: protein, 40S ribosomal protein S7-A

• Protein: Name: 40S ribosomal protein S7-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 21.658209 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #10: protein, 40S ribosomal protein S8-A

• Protein: Name: 40S ribosomal protein S8-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.537803 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #11: protein, 40S ribosomal protein S9-A

• Protein: Name: 40S ribosomal protein S9-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.487893 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #12: protein, 40S ribosomal protein S11-A

• Protein: Name: 40S ribosomal protein S11-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.785934 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #13: protein, 40S ribosomal protein S13

• Protein: Name: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.059945 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #14: protein, 40S ribosomal protein S14-A

• Protein: Name: 40S ribosomal protein S14-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 14.562655 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #15: protein, 40S ribosomal protein S16-A

• Protein: Name: 40S ribosomal protein S16-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.87749 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #16: protein, 40S ribosomal protein S22-B

• Protein: Name: 40S ribosomal protein S22-BRibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 14.650062 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #17: protein, 40S ribosomal protein S23-A

• Protein: Name: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 16.073896 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #18: protein, 40S ribosomal protein S24-A

• Protein: Name: 40S ribosomal protein S24-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.362848 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #19: protein, 40S ribosomal protein S27-A

• Protein: Name: 40S ribosomal protein S27-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 8.893391 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #20: protein, 40S ribosomal protein S28-A

• Protein: Name: 40S ribosomal protein S28-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 7.605847 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #21: protein, rRNA 2'-O-methyltransferase fibrillarin

• Protein: Name: rRNA 2'-O-methyltransferase fibrillarin / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 34.525418 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #22: protein, Nucleolar protein 56

• Protein: Name: Nucleolar protein 56Nucleolus / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 56.961152 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #23: protein, Nucleolar protein 58

• Protein: Name: Nucleolar protein 58Nucleolus / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 57.060344 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #24: protein, Ribosomal RNA-processing protein 9

• Protein: Name: Ribosomal RNA-processing protein 9 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 65.146969 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #25: protein, 13 kDa ribonucleoprotein-associated protein

• Protein: Name: 13 kDa ribonucleoprotein-associated protein / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 13.582855 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #26: protein, U3 small nucleolar RNA-associated protein 4

• Protein: Name: U3 small nucleolar RNA-associated protein 4 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 87.909242 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #27: protein, U3 small nucleolar RNA-associated protein 5

• Protein: Name: U3 small nucleolar RNA-associated protein 5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 72.079445 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #28: protein, U3 small nucleolar RNA-associated protein 8

• Protein: Name: U3 small nucleolar RNA-associated protein 8 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 80.269648 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #29: protein, U3 small nucleolar RNA-associated protein 9

• Protein: Name: U3 small nucleolar RNA-associated protein 9 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 65.347254 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #30: protein, U3 small nucleolar RNA-associated protein 10

• Protein: Name: U3 small nucleolar RNA-associated protein 10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 200.298984 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #31: protein, U3 small nucleolar RNA-associated protein 15

• Protein: Name: U3 small nucleolar RNA-associated protein 15 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 57.765289 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #32: protein, NET1-associated nuclear protein 1

• Protein: Name: NET1-associated nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 101.341734 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #33: protein, Periodic tryptophan protein 2

• Protein: Name: Periodic tryptophan protein 2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 104.097039 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #34: protein, U3 small nucleolar RNA-associated protein 12

• Protein: Name: U3 small nucleolar RNA-associated protein 12 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 106.481133 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #35: protein, U3 small nucleolar RNA-associated protein 13

• Protein: Name: U3 small nucleolar RNA-associated protein 13 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 91.132562 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #36: protein, U3 small nucleolar RNA-associated protein 18

• Protein: Name: U3 small nucleolar RNA-associated protein 18 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 66.49425 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #37: protein, U3 small nucleolar RNA-associated protein 21

• Protein: Name: U3 small nucleolar RNA-associated protein 21 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 104.927844 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #38: protein, U3 small nucleolar RNA-associated protein 6

• Protein: Name: U3 small nucleolar RNA-associated protein 6 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 52.495277 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #39: protein, Bud site selection protein 21

• Protein: Name: Bud site selection protein 21 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 24.431016 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #40: protein, U3 small nucleolar RNA-associated protein 7

• Protein: Name: U3 small nucleolar RNA-associated protein 7 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 62.41857 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #41: protein, U3 small nucleolar RNA-associated protein 11

• Protein: Name: U3 small nucleolar RNA-associated protein 11 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 29.806348 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #42: protein, U3 small nucleolar RNA-associated protein MPP10

• Protein: Name: U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 67.042492 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #43: protein, U3 small nucleolar ribonucleoprotein protein IMP3

• Protein: Name: U3 small nucleolar ribonucleoprotein protein IMP3 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 21.928529 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #44: protein, U3 small nucleolar ribonucleoprotein protein IMP4

• Protein: Name: U3 small nucleolar ribonucleoprotein protein IMP4 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 33.536168 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #45: protein, Something about silencing protein 10

• Protein: Name: Something about silencing protein 10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 70.364398 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #46: protein, Protein SOF1

• Protein: Name: Protein SOF1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 56.888918 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #47: protein, rRNA-processing protein FCF2

• Protein: Name: rRNA-processing protein FCF2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 25.68924 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #48: protein, rRNA-processing protein FCF1

• Protein: Name: rRNA-processing protein FCF1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 21.650729 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #49: protein, Ribosome biogenesis protein ENP2

• Protein: Name: Ribosome biogenesis protein ENP2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 81.864172 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #50: protein, U3 small nucleolar ribonucleoprotein protein LCP5

• Protein: Name: U3 small nucleolar ribonucleoprotein protein LCP5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 40.864391 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #51: protein, rRNA biogenesis protein RRP5

• Protein: Name: rRNA biogenesis protein RRP5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 193.411422 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #52: protein, U3 small nucleolar RNA-associated protein 22

• Protein: Name: U3 small nucleolar RNA-associated protein 22 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 140.660141 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #53: protein, Ribosomal RNA-processing protein 7

• Protein: Name: Ribosomal RNA-processing protein 7 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 34.526441 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #54: protein, Ribosomal RNA small subunit methyltransferase NEP1

• Protein: Name: Ribosomal RNA small subunit methyltransferase NEP1 / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 27.936461 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #55: protein, Ribosome biogenesis protein BMS1

• Protein: Name: Ribosome biogenesis protein BMS1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 135.792281 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #56: protein, RNA 3'-terminal phosphate cyclase-like protein

• Protein: Name: RNA 3'-terminal phosphate cyclase-like protein / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 40.220559 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #57: protein, RNA cytidine acetyltransferase

• Protein: Name: RNA cytidine acetyltransferase / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 119.509445 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #58: protein, Nucleolar complex protein 14

• Protein: Name: Nucleolar complex protein 14 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 94.463195 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #59: protein, Nucleolar complex protein 4

• Protein: Name: Nucleolar complex protein 4 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 63.707844 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #60: protein, U3 small nucleolar RNA-associated protein 20

• Protein: Name: U3 small nucleolar RNA-associated protein 20 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 287.9155 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #61: protein, U3 small nucleolar RNA-associated protein 14

• Protein: Name: U3 small nucleolar RNA-associated protein 14 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 103.18975 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #62: protein, Essential nuclear protein 1

• Protein: Name: Essential nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 55.207422 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #63: protein, Pno1

• Protein: Name: Pno1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 36.356477 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #64: protein, Protein BFR2

• Protein: Name: Protein BFR2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 61.285039 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #65: protein, Unassigned helices

• Protein: Name: Unassigned helices / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 29.549291 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #66: ligand, ZINC ION

• Ligand: Name: ZINC ION / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 6.540905 MDa

Component #67: ligand, GUANOSINE-5'-TRIPHOSPHATE

• Ligand: Name: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 0.52318 kDa

Component #68: ligand, MAGNESIUM ION

• Ligand: Name: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 2.430505 MDa

Experimental details

Sample preparation

• Specimen: Specimen state: Particle / Method: cryo EM
• Sample solution: Specimen conc.: 2 mg/mL / pH: 7.4
• Vitrification: Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Imaging: Microscope: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 2500.0 nm
• Specimen Holder: Model: FEI TITAN KRIOS AUTOGRID HOLDER
• Camera: Detector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

• Image acquisition: Number of digital images: 18028

Image processing

• Processing: Method: single particle reconstruction / Number of projections: 3050
• 3D reconstruction: Software: RELION / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Modeling #1

Input PDB model: 6LQP

6lqp

Output model

6lqr