EMDB-6695: Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-dep...

Basic information

• Entry: Database: EMDB / ID: EMD-6695
• Title: Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)

Sample

90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)

• (nucleic-acidNucleic acid) x 3
• rRNA 2'-O-methyltransferase fibrillarin
• (Nucleolar protein ...Nucleolus) x 2
• (Ribosomal RNA-processing protein ...) x 2
• 13 kDa ribonucleoprotein-associated protein
• Utp4
• Utp5
• Utp8
• Utp9
• (U3 small nucleolar RNA-associated protein ...) x 6
• Utp15
• Utp17
• (Ribosome biogenesis protein ...) x 2
• Periodic tryptophan protein 2
• Ribosomal RNA small subunit methyltransferase NEP1
• Essential nuclear protein 1
• Enp2
• KRR1 small subunit processome component
• (U3 small nucleolar ribonucleoprotein protein ...) x 2
• Mpp10,U3 small nucleolar RNA-associated protein MPP10
• Pre-rRNA-processing protein PNO1
• RNA 3'-terminal phosphate cyclase-like protein
• rRNA biogenesis protein RRP5
• Sof1
• (40S ribosomal protein ...) x 18
• Ubiquitin-40S ribosomal protein S31
• Utp7
• Utp11
• Utp20
• rRNA-processing protein FCF1
• (Helical domain ...) x 2
• Unassigned helices

Function / homology

Function:

CURI complex / t-UTP complex / 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 / 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) / box C/D RNP complex / rRNA primary transcript binding / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / protein localization to nucleolus / U4 snRNA binding / histone glutamine methylation / U3 snoRNA binding / 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) / enzyme activator activity / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / proteasome assembly / nuclear periphery / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / positive regulation of translational fidelity / maintenance of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / modification-dependent protein catabolic process / mRNA 5'-UTR binding / protein tag / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic stress granule / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / cytosolic small ribosomal subunit / unfolded protein binding / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / ATPase activity / GTPase activity / mRNA binding / GTP binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm

Domain/homology:

Bystin / Nucleic acid-binding, OB-fold / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp12 / Small-subunit processome, Utp21 / S15/NS1, RNA-binding / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc-binding ribosomal protein / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S12/S23 / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / 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 / Small-subunit processome, Utp13 / Ribosomal protein S30 / KOW / Ribosomal protein S5 domain 2-type fold, subgroup / PIN domain / Ribosomal protein S4e / Ribosomal protein S8e / Ribosomal protein S6e / Ribosomal protein S3Ae / WD40 repeat / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S11 / Ribosomal protein S24e / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / Nop domain / Ribosomal protein S27a / Ribosomal protein S5/S7, eukaryotic/archaeal / RNA-binding S4 domain / S1 domain / HAT (Half-A-TPR) repeat / ATPase, AAA-type, core / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / K Homology domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / NOL6/Upt22 / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S6, eukaryotic / Ribosomal protein L2, domain 2 / Fibrillarin / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Ribosomal RNA-processing protein 7, C-terminal domain / Anaphase-promoting complex subunit 4, WD40 domain / Periodic tryptophan protein 2 / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / RNA-binding domain, S1 / 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 / Ubiquitin-like domain superfamily / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Nrap protein domain 1 / Ribosomal protein S15P / Ribosomal protein S4/S9 / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L7Ae/L8/Nhp2 family / 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 / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / WD40 repeat, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold

Component:

rRNA biogenesis protein RRP5 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 22 / 13 kDa ribonucleoprotein-associated protein / 40S ribosomal protein S12 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 18 / rRNA-processing protein FCF1 / Ribosome biogenesis protein BMS1 / 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 / RNA 3'-terminal phosphate cyclase-like protein / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / 40S ribosomal protein S28-A / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / 40S ribosomal protein S8-A / 40S ribosomal protein S27-A / 40S ribosomal protein S4-A / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S14-A / 40S ribosomal protein S22-A / 40S ribosomal protein S23-A / 40S ribosomal protein S24-A / 40S ribosomal protein S30-A / 40S ribosomal protein S6-A / 40S ribosomal protein S1-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / Periodic tryptophan protein 2 / 40S ribosomal protein S5 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / Pre-rRNA-processing protein PNO1

• Biological species: Saccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
• Method: single particle reconstruction / cryo EM / Resolution: 8.7 Å
• Authors: Ye K / Zhu X / Sun Q
• Citation: Journal: Elife / Year: 2017; Title: Molecular architecture of the 90S small subunit pre-ribosome.; Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye / ; Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
• Validation Report: Summary, Full report, XML, About validation report

History

Deposition	Jan 13, 2017	-
Header (metadata) release	Mar 29, 2017	-
Map release	Mar 29, 2017	-
Update	Oct 9, 2019	-
Current status	Oct 9, 2019	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_6695.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.76 Å

Density

Contour Level	By AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum	-0.26489103 - 0.3423654
Average (Standard dev.)	0.00015627964 (±0.018068692)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 704.0 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.76	1.76	1.76
M x/y/z	400	400	400
origin x/y/z	0.000	0.000	0.000
length x/y/z	704.000	704.000	704.000
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	400	400	400
D min/max/mean	-0.265	0.342	0.000

Supplemental data

Sample components

Entire 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)

• Entire: Name: 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP); Number of components: 62

Component #1: protein, 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)

• Protein: Name: 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP); Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae (baker's yeast)

Component #2: nucleic-acid, U3 RNA

nucleic acid

Name: U3 RNA / 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: 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 #4: 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 #5: 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 #6: 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 #7: 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 #8: nucleic-acid, 5ETS RNA

nucleic acid

Name: 5ETS RNA / 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 #9: protein, Utp4

• Protein: Name: Utp4 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 66.059172 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #10: protein, Utp5

• Protein: Name: Utp5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 54.740609 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #11: protein, Utp8

• Protein: Name: Utp8 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 60.69775 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #12: protein, Utp9

• Protein: Name: Utp9 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 48.953438 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #13: protein, U3 small nucleolar RNA-associated protein 10,Utp10

• Protein: Name: U3 small nucleolar RNA-associated protein 10,Utp10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 173.592375 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #14: protein, Utp15

• Protein: Name: Utp15 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 43.676871 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #15: protein, Utp17

• Protein: Name: Utp17 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 76.271414 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #16: 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 #17: 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 #18: 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 #19: 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 #20: 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 #21: 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 #22: 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 #23: 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 #24: 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 #25: 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 #26: protein, Enp2

• Protein: Name: Enp2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 60.187137 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #27: protein, KRR1 small subunit processome component

• Protein: Name: KRR1 small subunit processome component / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 37.226254 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #28: 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 #29: 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 #30: protein, Mpp10,U3 small nucleolar RNA-associated protein MPP10

• Protein: Name: Mpp10,U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 54.936984 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #31: protein, Pre-rRNA-processing protein PNO1

• Protein: Name: Pre-rRNA-processing protein PNO1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 30.380623 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #32: 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 #33: 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 #34: protein, Sof1

• Protein: Name: Sof1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 41.634328 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #35: nucleic-acid, 18S ribosomal RNA

nucleic acid

Name: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ACAUGCUUAA AAUCUCGACC CUUUGGAAGA GAUGUAUUUA UUAGAUAAAA AAUCAAUGUC UUCGGACUCU UUGAUGAUUC AUAAUAACUU UUCGAAUCGC AUGGCCUUGU GCUGGCGAUG GUUCAUUCAA AUUUCUGCCC UAUCAACUUU CGAUGGUAGG AUAGUGGCCU ACCAUGGUUU CAACGGGUAA CGGGGAAUAA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCCAAGGA AGGCAGCAGG CGCGCAAAUU ACCCAAUCCU AAUUCAGGGA GGUAGUGACA AUAAAUAACG AUACAGGGCC CAUUCGGGUC UUGUAAUUGG AAUGAGUACA AUGUAAAUAC CUUAACGAGG AACAAUUGGA GGGCAAGUCU GGUGCCAGCA GCCGCGGUAA UUCCAGCUCC AAUAGCGUAU AUUAAAGUUG UUGCAGUUAA AAAGCUCGUA GUUGAACUUU GGGCCCGGUU GGCCGGUCCG AUUUUUUCGU GUACUGGAUU UCCAACGGGG CCUUUCCUUC UGGCUAACCU UGAGUCCUUG UGGCUCUUGG CGAACCAGGA CUUUUACUUU GAAAAAAUUA GAGUGUUCAA AGCAGGCGUA UUGCUCGAAU AUAUUAGCAU GGAAUAAUAG AAUAGGACGU UUGGUUCUAU UUUGUUGGUU UCUAGGACCA UCGUAAUGAU UAAUAGGGAC GGUCGGGGGC AUCAGUAUUC AAUUGUCAGA GGUGAAAUUC UUGGAUUUAU UGAAGACUAA CUACUGCGAA AGCAUUUGCC AAGGACGUUU UCAUUAAUCA AGAACGAAAG UUAGGGGAUC GAAGAUGAUC AGAUACCGUC GUAGUCUUAA CCAUAAACUA UGCCGACUAG GGAUCGGGUG GUGUUUUUUU AAUGACCCAC UCGGCACCUU ACGAGAAAUC AAAGUCUUUG GGUUCUGGGG GGAGUAUGGU CGCAAGGCUG AAACUUAAAG GAAUUGACGG AAGGGCACCA CCAGGAGUGG AGCCUGCGGC UUAAUUUGAC UCAACACGGG GAAACUCACC AGGUCCAGAC ACAAUAAGGA UUGACAGAUU GAGAGCUCUU UCUUGAUUUU GUGGGUGGUG GUGCAUGGCC GUUCUUAGUU GGUGGAGUGA UUUGUCUGCU UAAUUGCGAU AACGAACGAG ACCUUAACCU ACUAAAUAGU GGUGCUAGCA UUUGCUGGUU AUCCACUUCU UAGAGGGACU AUCGGUUUCA AGCCGAUGGA AGUUUGAGGC AAUAACAGGU CUGUGAUGCC CUUAGACGUU CUGGGCCGCA CGCGCGCUAC ACUGACGGAG CCAGCGAGUC UAACCUUGGC CGAGAGGUCU UGGUAAUCUU GUGAAACUCC GUCGUGCUGG GGAUAGAGCA UUGUAAUUAU UGCUCUUCAA CGAGGAAUUC CUAGUAAGCG CAAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUCUGCUUAG AGAAGGGGGC AACUCCAUCU CAGAGCGGAG AAUUUGGACA AACUUGGUCA UUUAGAGGAA CUAAAAGUCG UAACAAGGUU UCCGUAGGUG AACCUGCGGA AGGAUCAUUA AAGAAAUUUA AU

• Mass: Theoretical: 583.636562 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #36: 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 #37: 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 #38: 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 #39: 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 #40: 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 #41: 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 #42: 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 #43: 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 #44: protein, 40S ribosomal protein S12

• Protein: Name: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.488631 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #45: 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 #46: 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 #47: 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 #48: protein, 40S ribosomal protein S22-A

• Protein: Name: 40S ribosomal protein S22-ARibosome / 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 #49: 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 #50: 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 #51: 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 #52: 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 #53: protein, 40S ribosomal protein S30-A

• Protein: Name: 40S ribosomal protein S30-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 7.137541 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #54: protein, Ubiquitin-40S ribosomal protein S31

• Protein: Name: Ubiquitin-40S ribosomal protein S31 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.254227 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #55: protein, Utp7

• Protein: Name: Utp7 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 47.166211 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #56: protein, Utp11

• Protein: Name: Utp11 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 21.294152 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #57: protein, Utp20

• Protein: Name: Utp20 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 212.188828 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #58: 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 #59: protein, Ribosome biogenesis protein UTP30

• Protein: Name: Ribosome biogenesis protein UTP30 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 31.668939 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #60: protein, Helical domain protein

• Protein: Name: Helical domain protein / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 137.462422 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #61: protein, Helical domain protein

• Protein: Name: Helical domain protein / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 84.015695 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #62: protein, Unassigned helices

• Protein: Name: Unassigned helices / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 87.930383 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Experimental details

Sample preparation

• Specimen: Specimen state: Particle / Method: cryo EM
• Sample solution: pH: 8
• Vitrification: Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 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: 40 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Magnification: 45000.0 X (nominal), 79545.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4000.0 nm
• Specimen Holder: Model: FEI TITAN KRIOS AUTOGRID HOLDER
• Camera: Detector: OTHER

Image acquisition

• Image acquisition: Number of digital images: 2055

Image processing

• Processing: Method: single particle reconstruction / Applied symmetry: C₁ (asymmetric) / Number of projections: 30995 / Details: detector is Falcon III
• 3D reconstruction: Algorithm: BACK PROJECTION / Software: RELION / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

5wyj