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- EMDB-11363: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -

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Basic information

Entry
Database: EMDB / ID: EMD-11363
TitleCryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C
Map data
Sample90S pre-ribbosome state Dis-C
  • Nucleolar complex protein 14
  • Something about silencing protein 10
  • Noc4,Nucleolar complex protein 4,Noc4
  • rRNA-processing protein FCF1
  • U3 small nucleolar ribonucleoprotein protein IMP4
  • (U3 small nucleolar RNA-associated protein ...) x 2
  • Ribosome biogenesis protein BMS1
  • RNA 3'-terminal phosphate cyclase-like protein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Essential nuclear protein 1
  • Dimethyladenosine transferase
  • Pre-rRNA-processing protein PNO1
  • Rps5p
  • (40S ribosomal protein ...) x 18
  • (nucleic-acidNucleic acid) x 3
  • Probable ATP-dependent RNA helicase DHR1
  • (ligand) x 3
Function / homology
Function and homology information


18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / Noc4p-Nop14p complex / rRNA small subunit pseudouridine methyltransferase Nep1 / Mpp10 complex / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / Noc4p-Nop14p complex / rRNA small subunit pseudouridine methyltransferase Nep1 / Mpp10 complex / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / rRNA base methylation / single-stranded telomeric DNA binding / sno(s)RNA-containing ribonucleoprotein complex / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / 90S preribosome / preribosome, small subunit precursor / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / proteasome assembly / nuclear periphery / endoribonuclease activity / maintenance of translational fidelity / positive regulation of translational fidelity / enzyme activator activity / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / rRNA processing / cytoplasmic translation / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / ribosome / rRNA binding / RNA helicase / structural constituent of ribosome / mitochondrial matrix / cell cycle / translation / RNA helicase activity / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Bystin / Ribosomal protein S28e / Helicase, C-terminal / Ribosomal protein S3Ae / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal protein S8e / Ribosomal protein S4e / Ribosomal protein S9 / Ribosomal protein S8 ...Bystin / Ribosomal protein S28e / Helicase, C-terminal / Ribosomal protein S3Ae / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal protein S8e / Ribosomal protein S4e / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S27 / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S17/S11 / Ribosomal protein S13 / Ribosomal protein S5/S7 / RNA 3'-terminal phosphate cyclase / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / 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 / Helicase superfamily 1/2, ATP-binding domain / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Small-subunit processome, Utp14 / Ribosomal RNA adenine dimethylase / Zinc-binding ribosomal protein / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Helicase-associated domain / Nucleolar protein 14 / Sas10/Utp3/C1D / Brix domain / Ribosome biogenesis protein BMS1/TSR1, C-terminal / rRNA-processing protein Fcf1/Utp23 / Ribosomal protein S12/S23 / Ribosomal protein S11 / KOW / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Ribosomal protein S25 / ATPase, AAA-type, core / RNA-binding S4 domain / PIN domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Ribosomal protein S24e / Ribosomal protein S6, eukaryotic / Ribosomal protein L2, domain 2 / Domain of unknown function DUF1605 / Ribosomal protein S7 domain superfamily / Alpha/beta knot methyltransferases / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S28e conserved site / RNA-binding S4 domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / rRNA-processing protein Fcf1, PIN domain / Ribosome biogenesis protein Bms1, N-terminal / in:ipr038111: / Ribosomal protein S4e, central domain superfamily / Ribosome biogenesis protein Bms1/Tsr1 / Pre-rRNA-processing protein PNO1-like / Krr1, KH1 domain / Ribosomal protein S4, KOW domain / U3 snoRNP protein/Ribosome production factor 1 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S17, archaeal/eukaryotic / RNA 3'-terminal phosphate cyclase type 2 / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Sas10 C-terminal domain / Ribosomal protein S17, conserved site / Ribosomal protein S9, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal RNA adenine methylase transferase, conserved site
rRNA-processing protein FCF1 / Dimethyladenosine transferase / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar ribonucleoprotein protein IMP4 / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar RNA-associated protein 14 / RNA 3'-terminal phosphate cyclase-like protein / Ribosomal RNA small subunit methyltransferase NEP1 / 40S ribosomal protein S27-A / Ribosome biogenesis protein BMS1 ...rRNA-processing protein FCF1 / Dimethyladenosine transferase / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar ribonucleoprotein protein IMP4 / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar RNA-associated protein 14 / RNA 3'-terminal phosphate cyclase-like protein / Ribosomal RNA small subunit methyltransferase NEP1 / 40S ribosomal protein S27-A / Ribosome biogenesis protein BMS1 / Something about silencing protein 10 / 40S ribosomal protein S25-A / 40S ribosomal protein S28-A / Nucleolar complex protein 14 / Essential nuclear protein 1 / 40S ribosomal protein S5 / 40S ribosomal protein S1-A / 40S ribosomal protein S7-A / 40S ribosomal protein S18-A / 40S ribosomal protein S16-A / 40S ribosomal protein S11-A / 40S ribosomal protein S8-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S24-A / 40S ribosomal protein S23-A / 40S ribosomal protein S22-A / 40S ribosomal protein S19-A / 40S ribosomal protein S14-A / 40S ribosomal protein S13 / 40S ribosomal protein S9-A / Pre-rRNA-processing protein PNO1
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCheng J / Lau B / Venuta GL / Berninghausen O / Hurt E / Beckmann R
CitationJournal: Science / Year: 2020
Title: 90 pre-ribosome transformation into the primordial 40 subunit.
Authors: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann /
Abstract: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 9, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zqg
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11363.png

Downloads & links

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Map

FileDownload / File: emd_11363.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 480 pix.
= 508.32 Å		1.06 Å/pix.
x 480 pix.
= 508.32 Å		1.06 Å/pix.
x 480 pix.
= 508.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.043471146 - 0.09912797
Average (Standard dev.)0.0001424978 (±0.0018802981)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 508.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.320508.320508.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ100115122
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0430.0990.000

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Supplemental data

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Additional map: Multibody refine focus 3domain

Fileemd_11363_additional.map
AnnotationMultibody refine focus 3domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire 90S pre-ribbosome state Dis-C

EntireName: 90S pre-ribbosome state Dis-C / Number of components: 40

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Component #1: protein, 90S pre-ribbosome state Dis-C

ProteinName: 90S pre-ribbosome state Dis-C / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #2: protein, Nucleolar complex protein 14

ProteinName: Nucleolar complex protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.463195 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: protein, Something about silencing protein 10

ProteinName: Something about silencing protein 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 70.364398 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, Noc4,Nucleolar complex protein 4,Noc4

ProteinName: Noc4,Nucleolar complex protein 4,Noc4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.707844 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #5: protein, rRNA-processing protein FCF1

ProteinName: rRNA-processing protein FCF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.650729 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #6: protein, U3 small nucleolar ribonucleoprotein protein IMP4

ProteinName: U3 small nucleolar ribonucleoprotein protein IMP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.536168 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, U3 small nucleolar RNA-associated protein MPP10

ProteinName: U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.042492 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, Ribosome biogenesis protein BMS1

ProteinName: Ribosome biogenesis protein BMS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 135.792281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, RNA 3'-terminal phosphate cyclase-like protein

ProteinName: RNA 3'-terminal phosphate cyclase-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.220559 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, Ribosomal RNA small subunit methyltransferase NEP1

ProteinName: Ribosomal RNA small subunit methyltransferase NEP1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.936461 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, Essential nuclear protein 1

ProteinName: Essential nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.207422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, Dimethyladenosine transferase

ProteinName: Dimethyladenosine transferase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.003836 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, Pre-rRNA-processing protein PNO1

ProteinName: Pre-rRNA-processing protein PNO1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.380623 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, Rps5p

ProteinName: Rps5p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.0726 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: 40S ribosomal protein S16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.87749 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, 40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18

ProteinName: 40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18Ribosome
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.303852 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #17: protein, 40S ribosomal protein S19-A

ProteinName: 40S ribosomal protein S19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.942125 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, 40S ribosomal protein S28-A

ProteinName: 40S ribosomal protein S28-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.605847 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: nucleic-acid, 18S rRNA

nucleic acidName: 18S rRNA18S 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 ...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 CGCAAGGCUA 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 ACCGAUUUCC AUCUCAGAGC GGAGAAUUUG GACAAACUUG GUCAUUUAGA GGAACUAAAA GUCGUAACAA GGUUUCCGUA GGUGAACCUG CGGAAGGAUC AUUAAAGA
MassTheoretical: 566.062188 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #20: protein, 40S ribosomal protein S1-A

ProteinName: 40S ribosomal protein S1-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.798467 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #21: protein, 40S ribosomal protein S4-A

ProteinName: 40S ribosomal protein S4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.46933 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #22: protein, 40S ribosomal protein S6-A

ProteinName: 40S ribosomal protein S6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.054486 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: protein, 40S ribosomal protein S7-A

ProteinName: 40S ribosomal protein S7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.658209 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #24: protein, 40S ribosomal protein S8-A

ProteinName: 40S ribosomal protein S8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #25: protein, 40S ribosomal protein S9-A

ProteinName: 40S ribosomal protein S9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.487893 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #26: protein, 40S ribosomal protein S11-A

ProteinName: 40S ribosomal protein S11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.785934 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #27: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.059945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #28: protein, 40S ribosomal protein S14-A

ProteinName: 40S ribosomal protein S14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.562655 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #29: protein, 40S ribosomal protein S25-A

ProteinName: 40S ribosomal protein S25-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.067272 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #30: protein, 40S ribosomal protein S22-A

ProteinName: 40S ribosomal protein S22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.650062 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #31: protein, 40S ribosomal protein S23-A

ProteinName: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.073896 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #32: protein, 40S ribosomal protein S24-A

ProteinName: 40S ribosomal protein S24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.362848 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #33: protein, 40S ribosomal protein S27-A

ProteinName: 40S ribosomal protein S27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.893391 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #34: protein, U3 small nucleolar RNA-associated protein 14

ProteinName: U3 small nucleolar RNA-associated protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 103.18975 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #35: protein, Probable ATP-dependent RNA helicase DHR1

ProteinName: Probable ATP-dependent RNA helicase DHR1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 145.171406 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #36: nucleic-acid, U3 snoRNA

nucleic acidName: U3 snoRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
(M7G)GUCGACGUA CUUCAUAGGA UCA
MassTheoretical: 7.460439 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #37: nucleic-acid, Poly-U RNA

nucleic acidName: Poly-U RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUUUUUU
MassTheoretical: 2.710535 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #38: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #39: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #40: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 39 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 44 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 102097
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Relion
FSC plot (resolution estimation)

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Atomic model buiding

Output model

6zqg

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