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- EMDB-0371: Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-0371
TitleCryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit
Map data
SampleEarly cytoplasmic-late (ECL) pre-60S ribosomal subunit
  • 60S ribosomal export protein NMD3
  • Ribosomal Protein uL1
  • (60S ribosomal protein ...) x 37
  • Nucleolar GTP-binding protein 1
  • Bud site selection protein 20
  • Ribosome biogenesis protein RLP24
  • Ribosome assembly factor MRT4
  • Eukaryotic translation initiation factor 6
  • UPF0642 protein YBL028C
  • (nucleic-acidNucleic acid) x 3
Function / homology
Function and homology information


maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / nuclear-transcribed mRNA catabolic process / positive regulation of ATPase activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / ribosomal large subunit binding / ribosomal subunit export from nucleus / ATPase activator activity / ribonucleoprotein complex assembly ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / nuclear-transcribed mRNA catabolic process / positive regulation of ATPase activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / ribosomal large subunit binding / ribosomal subunit export from nucleus / ATPase activator activity / ribonucleoprotein complex assembly / preribosome, large subunit precursor / response to cycloheximide / regulation of translational fidelity / negative regulation of mRNA splicing, via spliceosome / ribosomal large subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA / mature ribosome assembly / translation initiation factor activity / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / cytoplasmic translation / large ribosomal subunit rRNA binding / rRNA processing / macroautophagy / ribosome biogenesis / cytosolic large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / negative regulation of translation / rRNA binding / ribosome / ATPase binding / structural constituent of ribosome / nucleic acid binding / translation / mRNA binding / GTP binding / nucleolus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein L13e, conserved site / Ribosomal protein L29, conserved site / Zinc finger C2H2-type / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L21e, conserved site ...Ribosomal protein L13e, conserved site / Ribosomal protein L29, conserved site / Zinc finger C2H2-type / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Uncharacterised protein family UPF0642 / Ribosomal protein L3, conserved site / Ribosomal protein L25/L23 / Ribosomal protein L30, N-terminal / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L34Ae / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L13 / KOW / Ribosomal protein L24/L26, conserved site / Ribosomal protein L7, eukaryotic / GTP binding domain / Nmd3, N-terminal / Translation protein SH3-like domain superfamily / NOG, C-terminal / Translation protein, beta-barrel domain superfamily / Nucleolar GTP-binding protein 1, Rossman-fold domain / TRASH domain / Ribosomal protein L37ae/L37e / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L14P, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L19, eukaryotic / P-loop containing nucleoside triphosphate hydrolase / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / Ribosomal protein L15 / OBG-type guanine nucleotide-binding (G) domain / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosome assembly factor Mrt4 / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Zinc finger C2H2 superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / 60S ribosomal protein L4, C-terminal domain / Nucleolar GTP-binding protein 1 / Ribosomal protein L39e, conserved site / Zinc finger, double-stranded RNA binding / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L15e core domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L13, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L14P / Ribosomal protein L19/L19e / Ribosomal protein L39e / Ribosomal protein L31e / Ribosomal protein L18e / Ribosomal protein L21 superfamily / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily
UPF0642 protein YBL028C / 60S ribosomal protein L30 / 60S ribosomal protein L3 / 60S ribosomal protein L8-A / 60S ribosomal protein L5 / 60S ribosomal protein L16-A / Ribosome assembly factor MRT4 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / Eukaryotic translation initiation factor 6 ...UPF0642 protein YBL028C / 60S ribosomal protein L30 / 60S ribosomal protein L3 / 60S ribosomal protein L8-A / 60S ribosomal protein L5 / 60S ribosomal protein L16-A / Ribosome assembly factor MRT4 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / Eukaryotic translation initiation factor 6 / 60S ribosomal export protein NMD3 / 60S ribosomal protein L37-A / 60S ribosomal protein L38 / 60S ribosomal protein L34-A / 60S ribosomal protein L6-A / 60S ribosomal protein L21-A / Nucleolar GTP-binding protein 1 / Ribosome biogenesis protein RLP24 / Bud site selection protein 20 / 60S ribosomal protein L35-A / 60S ribosomal protein L4-A / 60S ribosomal protein L11-A / 60S ribosomal protein L19-A / 60S ribosomal protein L36-A / 60S ribosomal protein L28 / 60S ribosomal protein L25 / 60S ribosomal protein L39 / 60S ribosomal protein L7-A / 60S ribosomal protein L9-A / 60S ribosomal protein L17-A / 60S ribosomal protein L26-A / 60S ribosomal protein L33-A / 60S ribosomal protein L29 / 60S ribosomal protein L18-A / 60S ribosomal protein L15-A / 60S ribosomal protein L22-A / 60S ribosomal protein L27-A / 60S ribosomal protein L31-A / 60S ribosomal protein L20-A / 60S ribosomal protein L43-A / 60S ribosomal protein L42-A / 60S ribosomal protein L23-A / 60S ribosomal protein L2-A / 60S ribosomal protein L13-A
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhou Y / Musalgaonkar S / Johnson AW / Taylor DW
Funding support United States, 5 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR160088 United States
Army Research OfficeW911NF-15-0120 United States
Robert A. Welch FoundationF-1938 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127127 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53655 United States
CitationJournal: Nat Commun / Year: 2019
Title: Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.
Authors: Yi Zhou / Sharmishtha Musalgaonkar / Arlen W Johnson / David W Taylor /
Abstract: The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the ...The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome.
Validation ReportPDB-ID: 6n8l

SummaryFull reportAbout validation report
History
DepositionNov 29, 2018-
Header (metadata) releaseFeb 13, 2019-
Map releaseMar 13, 2019-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n8l
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0371.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å
1.1 Å/pix.
x 384 pix.
= 422.4 Å
1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07655697 - 0.14487666
Average (Standard dev.)0.00013052243 (±0.007450343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0770.1450.000

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Supplemental data

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Sample components

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Entire Early cytoplasmic-late (ECL) pre-60S ribosomal subunit

EntireName: Early cytoplasmic-late (ECL) pre-60S ribosomal subunit
Number of components: 49

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Component #1: protein, Early cytoplasmic-late (ECL) pre-60S ribosomal subunit

ProteinName: Early cytoplasmic-late (ECL) pre-60S ribosomal subunit
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #2: protein, 60S ribosomal export protein NMD3

ProteinName: 60S ribosomal export protein NMD3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.167047 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: protein, Ribosomal Protein uL1

ProteinName: Ribosomal Protein uL1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.485723 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, 60S ribosomal protein L2-A

ProteinName: 60S ribosomal protein L2-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.463574 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.761666 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #6: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.850793 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, Nucleolar GTP-binding protein 1

ProteinName: Nucleolar GTP-binding protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.531227 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, 60S ribosomal protein L4-A

ProteinName: 60S ribosomal protein L4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.159125 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.430364 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, 60S ribosomal protein L31-A

ProteinName: 60S ribosomal protein L31-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.980158 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, 60S ribosomal protein L6-A

ProteinName: 60S ribosomal protein L6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.000564 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.809441 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, 60S ribosomal protein L7-A

ProteinName: 60S ribosomal protein L7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.686281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, 60S ribosomal protein L33-A

ProteinName: 60S ribosomal protein L33-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.17713 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, 60S ribosomal protein L8-A

ProteinName: 60S ribosomal protein L8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.17582 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, 60S ribosomal protein L34-A

ProteinName: 60S ribosomal protein L34-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.673196 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, Bud site selection protein 20

ProteinName: Bud site selection protein 20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.546982 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, 60S ribosomal protein L9-A

ProteinName: 60S ribosomal protein L9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.605061 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: protein, 60S ribosomal protein L35-A

ProteinName: 60S ribosomal protein L35-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.94264 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: protein, 60S ribosomal protein L36-A

ProteinName: 60S ribosomal protein L36-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.151259 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #21: protein, 60S ribosomal protein L37-A

ProteinName: 60S ribosomal protein L37-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.877395 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #22: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.845561 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: protein, 60S ribosomal protein L13-A

ProteinName: 60S ribosomal protein L13-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.604164 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #24: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.35864 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #25: protein, 60S ribosomal protein L14-A

ProteinName: 60S ribosomal protein L14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.195066 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #26: protein, 60S ribosomal protein L43-A

ProteinName: 60S ribosomal protein L43-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.112952 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #27: protein, 60S ribosomal protein L15-A

ProteinName: 60S ribosomal protein L15-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.482357 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #28: protein, Ribosome biogenesis protein RLP24

ProteinName: Ribosome biogenesis protein RLP24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.02765 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #29: protein, 60S ribosomal protein L16-A

ProteinName: 60S ribosomal protein L16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.247227 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #30: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.589518 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #31: protein, 60S ribosomal protein L18-A

ProteinName: 60S ribosomal protein L18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.609252 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #32: protein, 60S ribosomal protein L19-A

ProteinName: 60S ribosomal protein L19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.762316 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #33: protein, 60S ribosomal protein L20-A

ProteinName: 60S ribosomal protein L20-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.478852 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #34: protein, 60S ribosomal protein L21-A

ProteinName: 60S ribosomal protein L21-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.279266 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #35: protein, 60S ribosomal protein L22-A

ProteinName: 60S ribosomal protein L22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.711359 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #36: protein, 60S ribosomal protein L23-A

ProteinName: 60S ribosomal protein L23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.49395 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #37: protein, Ribosome assembly factor MRT4

ProteinName: Ribosome assembly factor MRT4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.098012 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #38: protein, 60S ribosomal protein L25

ProteinName: 60S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.787612 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #39: protein, 60S ribosomal protein L26-A

ProteinName: 60S ribosomal protein L26-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.265784 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #40: protein, Eukaryotic translation initiation factor 6

ProteinName: Eukaryotic translation initiation factor 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.476605 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #41: protein, 60S ribosomal protein L27-A

ProteinName: 60S ribosomal protein L27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.56836 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #42: protein, UPF0642 protein YBL028C

ProteinName: UPF0642 protein YBL028C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.435429 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #43: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.764828 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #44: protein, 60S ribosomal protein L11-A

ProteinName: 60S ribosomal protein L11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.755691 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #45: protein, 60S ribosomal protein L42-A

ProteinName: 60S ribosomal protein L42-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.246658 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #46: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.691884 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #47: nucleic-acid, Saccharomyces cerevisiae S288C 35S pre-ribosomal RN...

nucleic acidName: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAAC GGCGAGUGAA GCGGCAAAAG CUCAAAUUUG AAAUCUGGUA CCUUCGGUGC CCGAGUUGUA AUUUGGAGAG GGCAACUUUG ...Sequence:
GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAAC GGCGAGUGAA GCGGCAAAAG CUCAAAUUUG AAAUCUGGUA CCUUCGGUGC CCGAGUUGUA AUUUGGAGAG GGCAACUUUG GGGCCGUUCC UUGUCUAUGU UCCUUGGAAC AGGACGUCAU AGAGGGUGAG AAUCCCGUGU GGCGAGGAGU GCGGUUCUUU GUAAAGUGCC UUCGAAGAGU CGAGUUGUUU GGGAAUGCAG CUCUAAGUGG GUGGUAAAUU CCAUCUAAAG CUAAAUAUUG GCGAGAGACC GAUAGCGAAC AAGUACAGUG AUGGAAAGAU GAAAAGAACU UUGAAAAGAG AGUGAAAAAG UACGUGAAAU UGUUGAAAGG GAAGGGCAUU UGAUCAGACA UGGUGUUUUG UGCCCUCUGC UCCUUGUGGG UAGGGGAAUC UCGCAUUUCA CUGGGCCAGC AUCAGUUUUG GUGGCAGGAU AAAUCCAUAG GAAUGUAGCU UGCCUCGGUA AGUAUUAUAG CCUGUGGGAA UACUGCCAGC UGGGACUGAG GACUGCGACG UAAGUCAAGG AUGCUGGCAU AAUGGUUAUA UGCCGCCCGU CUUGAAACAC GGACCAAGGA GUCUAACGUC UAUGCGAGUG UUUGGGUGUA AAACCCAUAC GCGUAAUGAA AGUGAACGUA GGUUGGGGCC UCGCAAGAGG UGCACAAUCG ACCGAUCCUG AUGUCUUCGG AUGGAUUUGA GUAAGAGCAU AGCUGUUGGG ACCCGAAAGA UGGUGAACUA UGCCUGAAUA GGGUGAAGCC AGAGGAAACU CUGGUGGAGG CUCGUAGCGG UUCUGACGUG CAAAUCGAUC GUCGAAUUUG GGUAUAGGGG CGAAAGACUA AUCGAACCAU CUAGUAGCUG GUUCCUGCCG AAGUUUCCCU CAGGAUAGCA GAAGCUCGUA UCAGUUUUAU GAGGUAAAGC GAAUGAUUAG AGGUUCCGGG GUCGAAAUGA CCUUGACCUA UUCUCAAACU UUAAAUAUGU AAGAAGUCCU UGUUACUUAA UUGAACGUGG ACAUUUGAAU GAAGAGCUUU UAGUGGGCCA UUUUUGGUAA GCAGAACUGG CGAUGCGGGA UGAACCGAAC GUAGAGUUAA GGUGCCGGAA UACACGCUCA UCAGACACCA CAAAAGGUGU UAGUUCAUCU AGACAGCCGG ACGGUGGCCA UGGAAGUCGG AAUCCGCUAA GGAGUGUGUA ACAACUCACC GGCCGAAUGA ACUAGCCCUG AAAAUGGAUG GCGCUCAAGC GUGUUACCUA UACUCUACCG UCAGGGUUGA UAUGAUGCCC UGACGAGUAG GCAGGCGUGG AGGUCAGUGA CGAAGCCUAG ACCGUAAGGU CGGGUCGAAC GGCCUCUAGU GCAGAUCUUG GUGGUAGUAG CAAAUAUUCA AAUGAGAACU UUGAAGACUG AAGUGGGGAA AGGUUCCACG UCAACAGCAG UUGGACGUGG GUUAGUCGAU CCUAAGAGAU GGGGAAGCUC CGUUUCAAAG GCCUGAUUUU AUGCAGGCCA CCAUCGAAAG GGAAUCCGGU UAAGAUUCCG GAACCUGGAU AUGGAUUCUU CACGGUAACG UAACUGAAUG UGGAGACGUC GGCGCGAGCC CUGGGAGGAG UUAUCUUUUC UUCUUAACAG CUUAUCACCC CGGAAUUGGU UUAUCCGGAG AUGGGGUCUU AUGGCUGGAA GAGGCCAGCA CCUUUGCUGG CUCCGGUGCG CUUGUGACGG CCCGUGAAAA UCCACAGGAA GGAAUAGUUU UCAUGCCAGG UCGUACUGAU AACCGCAGCA GGUCUCCAAG GUGAACAGCC UCUAGUUGAU AGAAUAAUGU AGAUAAGGGA AGUCGGCAAA AUAGAUCCGU AACUUCGGGA UAAGGAUUGG CUCUAAGGGU CGGGUAGUGA GGGCCUUGGU CAGACGCAGC GGGCGUGCUU GUGGACUGCU UGGUGGGGCU UGCUCUGCUA GGCGGACUAC UUGCGUGCCU UGUUGUAGAC GGCCUUGGUA GGUCUCUUGU AGACCGUCGC UUGCUACAAU UAACGAUCAA CUUAGAACUG GUACGGACAA GGGGAAUCUG ACUGUCUAAU UAAAACAUAG CAUUGCGAUG GUCAGAAAGU GAUGUUGACG CAAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAC CAAGCGCGGG UAAACGGCGG GAGUAACUAU GACUCUCUUA AGGUAGCCAA AUGCCUCGUC AUCUAAUUAG UGACGCGCAU GAAUGGAUUA ACGAGAUUCC CACUGUCCCU AUCUACUAUC UAGCGAAACC ACAGCCAAGG GAACGGGCUU GGCAGAAUCA GCGGGGAAAG AAGACCCUGU UGAGCUUGAC UCUAGUUUGA CAUUGUGAAG AGACAUAGAG GGUGUAGAAU AAGUGGGAGC UUCGGCGCCA GUGAAAUACC ACUACCUUUA UAGUUUCUUU ACUUAUUCAA UGAAGCGGAG CUGGAAUUCA UUUUCCACGU UCUAGCAUUC AAGGUCCCAU UCGGGGCUGA UCCGGGUUGA AGACAUUGUC AGGUGGGGAG UUUGGCUGGG GCGGCACAUC UGUUAAACGA UAACGCAGAU GUCCUAAGGG GGGCUCAUGG AGAACAGAAA UCUCCAGUAG AACAAAAGGG UAAAAGCCCC CUUGAUUUUG AUUUUCAGUG UGAAUACAAA CCAUGAAAGU GUGGCCUAUC GAUCCUUUAG UCCCUCGGAA UUUGAGGCUA GAGGUGCCAG AAAAGUUACC ACAGGGAUAA CUGGCUUGUG GCAGUCAAGC GUUCAUAGCG ACAUUGCUUU UUGAUUCUUC GAUGUCGGCU CUUCCUAUCA UACCGAAGCA GAAUUCGGUA AGCGUUGGAU UGUUCACCCA CUAAUAGGGA ACGUGAGCUG GGUUUAGACC GUCGUGAGAC AGGUUAGUUU UACCCUACUG AUGAAUGUUA CCGCAAUAGU AAUUGAACUU AGUACGAGAG GAACAGUUCA UUCGGAUAAU UGGUUUUUGC GGCUGUCUGA UCAGGCAUUG CCGCGAAGCU ACCAUCCGCU GGAUUAUGGC UGAACGCCUC UAAGUCAGAA UCCAUGCUAG AACGCGGUGA UUUCUUUGCU CCACACAAUA UAGAUGGAUA CGAAUAAGGC GUCCUUGUGG CGUCGCUGAA CCAUAGCAGG CUAGCAACGG UGCACUUGGC GGAAAGGCCU UGGGUGCUUG CUGGCGAAUU GCAAUGUCAU UUUGCGUGGG GAUAAAUCAU UUGUAUACGA CUUAGAUGUA CAACGGGGUA UUGUAAGCAG UAGAGUAGCC UUGUUGUUAC GAUCUGCUGA GAUUAAGCCU UUGUUGUCUG AUUUGU
MassTheoretical: 1.097493875 MDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #48: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGGU GACCAUACGC GAAACUCAGG UGCUGCAAUC U
MassTheoretical: 38.951105 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #49: nucleic-acid, 5.8S rRNA

nucleic acidName: 5.8S rRNA5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAACUUUCAA CAACGGAUCU CUUGGUUCUC GCAUCGAUGA AGAACGCAGC GAAAUGCGAU ACGUAAUGUG AAUUGCAGAA UUCCGUGAAU CAUCGAAUCU UUGAACGCAC AUUGCGCCCC UUGGUAUUCC AGGGGGCAUG CCUGUUUGAG CGUCAUUU
MassTheoretical: 50.682922 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 42030
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 3JCT
Output model

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