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- PDB-6ylh: Rix1-Rea1 pre-60S particle - full composite structure -

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Entry
Database: PDB / ID: 6ylh
TitleRix1-Rea1 pre-60S particle - full composite structure
Components
  • (60S ribosomal protein ...) x 37
  • (Nucleolar GTP-binding protein ...) x 2
  • (Pre-rRNA-processing protein ...) x 3
  • (Ribosome assembly ...) x 2
  • (Ribosome biogenesis protein ...) x 3
  • 25S rRNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Bud site selection protein 20
  • Eukaryotic translation initiation factor 6
  • Midasin
  • Nuclear GTP-binding protein NUG1
  • Probable metalloprotease ARX1
  • Protein SDA1
  • UPF0642 protein YBL028C
  • rRNA-processing protein CGR1
KeywordsRIBOSOME / pre-60S / Biogenesis / LSU / Large subunit / ribosome assembly
Function / homology
Function and homology information


Rix1 complex / regulation of ribosomal subunit export from nucleus / protein-RNA complex remodeling / regulation of DNA-dependent DNA replication initiation / nuclear pre-replicative complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / 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 / traversing start control point of mitotic cell cycle ...Rix1 complex / regulation of ribosomal subunit export from nucleus / protein-RNA complex remodeling / regulation of DNA-dependent DNA replication initiation / nuclear pre-replicative complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / 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 / traversing start control point of mitotic cell cycle / Hydrolases / 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) / ribosomal large subunit binding / pre-mRNA 5'-splice site binding / ATPase activator activity / ribosomal subunit export from nucleus / preribosome, large subunit precursor / ribonucleoprotein complex assembly / negative regulation of mRNA splicing, via spliceosome / regulation of translational fidelity / 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 / mature ribosome assembly / maturation of LSU-rRNA / translation initiation factor activity / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / metallopeptidase activity / rRNA processing / large ribosomal subunit rRNA binding / macroautophagy / cytoplasmic translation / actin cytoskeleton organization / ribosome biogenesis / large ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / ribosome binding / 5S rRNA binding / negative regulation of translation / ribosome / rRNA binding / ATPase binding / nucleic acid binding / structural constituent of ribosome / translation / ATPase activity / cell cycle / GTPase activity / mRNA binding / GTP binding / nucleolus / chromatin binding / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein L32e, conserved site / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Nucleic acid-binding, OB-fold / Pre-rRNA-processing protein RIX1, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Nucleolar GTP-binding protein 2, N-terminal domain / NLE / NOG, C-terminal / Uncharacterised domain NUC130/133, N-terminal ...Ribosomal protein L32e, conserved site / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Nucleic acid-binding, OB-fold / Pre-rRNA-processing protein RIX1, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Nucleolar GTP-binding protein 2, N-terminal domain / NLE / NOG, C-terminal / Uncharacterised domain NUC130/133, N-terminal / Ribosomal protein L30, N-terminal / Ribosomal protein L25/L23 / ATPase, dynein-related, AAA domain / Zinc finger C2H2-type / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Guanine nucleotide-binding protein-like 3, N-terminal domain / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L19/L19e, domain 1 / Armadillo-type fold / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Midasin / Zinc-binding ribosomal protein / Ribosomal protein L30, conserved site / Ribosomal protein L26/L24, eukaryotic/archaeal / AAA+ ATPase domain / Matrin/U1-C-like, C2H2-type zinc finger / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L5 eukaryotic/L18 archaeal / Cgr1-like / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L13 / Ribosomal protein L37ae/L37e / KOW / Ribosomal protein L24/L26, conserved site / Ribosomal protein L7, eukaryotic / GTP binding domain / SDA1 domain / Ribosomal protein L34Ae / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / Nucleolar GTP-binding protein 1, Rossman-fold domain / TRASH domain / WD40-repeat-containing domain / Ribosomal protein L34e, conserved site / Translation initiation factor IF6 / Ribosomal protein L13, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Zinc finger, double-stranded RNA binding / Ribosome biogenesis protein Alb1 / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Pre-rRNA-processing protein Ipi1, N-terminal / Ribosomal protein L15e core domain superfamily / Nucleolar GTP-binding protein 1 / Nucleolar GTP-binding protein 2 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L18e, conserved site / Ribosomal protein L29, conserved site / WD40 repeat, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / 60S ribosomal protein L4, C-terminal domain / 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 L18e/L15P / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L14e domain / Ribosomal protein L38e / Sigma-54 interaction domain, ATP-binding site 1
Nucleolar GTP-binding protein 2 / Pre-rRNA-processing protein RIX1 / rRNA-processing protein CGR1 / 60S ribosomal protein L38 / 60S ribosomal protein L37-A / Nuclear GTP-binding protein NUG1 / Ribosome assembly factor MRT4 / UPF0642 protein YBL028C / 60S ribosomal protein L32 / 60S ribosomal protein L14-A ...Nucleolar GTP-binding protein 2 / Pre-rRNA-processing protein RIX1 / rRNA-processing protein CGR1 / 60S ribosomal protein L38 / 60S ribosomal protein L37-A / Nuclear GTP-binding protein NUG1 / Ribosome assembly factor MRT4 / UPF0642 protein YBL028C / 60S ribosomal protein L32 / 60S ribosomal protein L14-A / 60S ribosomal protein L5 / 60S ribosomal protein L16-A / Protein SDA1 / gb:1331532632: / Pre-rRNA-processing protein IPI3 / 60S ribosomal protein L34-A / 60S ribosomal protein L6-A / 60S ribosomal protein L21-A / Nucleolar GTP-binding protein 1 / Probable metalloprotease ARX1 / Ribosome biogenesis protein RLP24 / Bud site selection protein 20 / Midasin / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L13-A / gb:834774822: / 60S ribosomal protein L8-A / Ribosome assembly protein 4 / Pre-rRNA-processing protein IPI1 / 60S ribosomal protein L3 / 60S ribosomal protein L22-A / Ribosome biogenesis protein ALB1 / Ribosome biogenesis protein NSA2 / 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 L36-A / 60S ribosomal protein L15-A / 60S ribosomal protein L11-A / 60S ribosomal protein L30 / 60S ribosomal protein L27-A / 60S ribosomal protein L31-A / 60S ribosomal protein L20-A / 60S ribosomal protein L43-A / 60S ribosomal protein L23-A / 60S ribosomal protein L1-A / 60S ribosomal protein L2-A / 60S ribosomal protein L18-A / 60S ribosomal protein L12-A / 60S ribosomal protein L19-A / 60S ribosomal protein L35-A / 60S ribosomal protein L4-A / gb:1329886537:
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKater, L. / Beckmann, R.
CitationJournal: Mol. Cell / Year: 2020
Title: Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Authors: Lukas Kater / Valentin Mitterer / Matthias Thoms / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering ...Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1-Ipi3 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
1: 25S rRNA
2: 5.8S rRNA
3: 5S rRNA
4: Probable metalloprotease ARX1
5: rRNA-processing protein CGR1
A: 60S ribosomal protein L2-A
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4-A
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6-A
F: 60S ribosomal protein L7-A
G: 60S ribosomal protein L8-A
H: 60S ribosomal protein L9-A
I: Bud site selection protein 20
J: 60S ribosomal protein L11-A
K: Pre-rRNA-processing protein IPI1
L: 60S ribosomal protein L13-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L15-A
O: 60S ribosomal protein L16-A
P: 60S ribosomal protein L17-A
Q: 60S ribosomal protein L18-A
R: 60S ribosomal protein L19-A
S: 60S ribosomal protein L20-A
T: 60S ribosomal protein L21-A
U: 60S ribosomal protein L22-A
V: 60S ribosomal protein L23-A
W: Ribosome assembly factor MRT4
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28
b: Nucleolar GTP-binding protein 1
c: Ribosome biogenesis protein ALB1
d: 60S ribosomal protein L31-A
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
g: 60S ribosomal protein L34-A
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
l: 60S ribosomal protein L39
m: Nucleolar GTP-binding protein 2
n: 60S ribosomal protein L30
o: 60S ribosomal protein L1-A
p: 60S ribosomal protein L43-A
q: 60S ribosomal protein L12-A
r: Ribosome biogenesis protein NSA2
s: Nuclear GTP-binding protein NUG1
t: Protein SDA1
u: Ribosome biogenesis protein RLP24
x: Ribosome assembly protein 4
y: Eukaryotic translation initiation factor 6
z: UPF0642 protein YBL028C
v: Midasin
w: Pre-rRNA-processing protein IPI3
0: Pre-rRNA-processing protein IPI3
6: Pre-rRNA-processing protein RIX1
7: Pre-rRNA-processing protein RIX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,358,97268
Polymers3,357,61660
Non-polymers1,3578
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain 25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 834774822
#2: RNA chain 5.8S rRNA / 5.8S ribosomal RNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1331532632
#3: RNA chain 5S rRNA / 5S ribosomal RNA / 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1329886537

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Protein , 8 types, 8 molecules 45Istyzv

#4: Protein Probable metalloprotease ARX1 / Associated with ribosomal export complex protein 1


Mass: 65290.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03862, Hydrolases
#5: Protein rRNA-processing protein CGR1 / Coiled-coil growth-regulated protein 1


Mass: 14460.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53188
#14: Protein Bud site selection protein 20


Mass: 18546.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q08004
#50: Protein Nuclear GTP-binding protein NUG1 / Nuclear GTPase 1


Mass: 57798.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40010
#51: Protein Protein SDA1 / Severe depolymerization of actin protein 1


Mass: 86755.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53313
#54: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12522
#55: Protein UPF0642 protein YBL028C


Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38202
#56: Protein Midasin / Dynein-related AAA-ATPase REA1 / MIDAS-containing protein / Ribosome export/assembly protein 1


Mass: 559951.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12019

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60S ribosomal protein ... , 37 types, 37 molecules ABCDEFGHJLMNOPQRSTUVXYZadefghi...

#6: Protein 60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6 / Ribosome


Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX45
#7: Protein 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1 /


Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14126
#8: Protein 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2 / Ribosome


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10664
#9: Protein 60S ribosomal protein L5 / / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3 /


Mass: 33764.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26321
#10: Protein 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16 / Ribosome


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02326
#11: Protein 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8 / Ribosome


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05737
#12: Protein 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5 / Ribosome


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#13: Protein 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11 / Ribosome


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05738
#15: Protein 60S ribosomal protein L11-A / Ribosome / L16 / Large ribosomal subunit protein uL5-A / RP39 / YL22 / Ribosome


Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W9
#17: Protein 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A / Ribosome


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12690
#18: Protein 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A / Ribosome


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36105
#19: Protein 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18 / Ribosome


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05748
#20: Protein 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15 / Ribosome


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26784
#21: Protein 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17 / Ribosome


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05740
#22: Protein 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28 / Ribosome


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX49
#23: Protein 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14 / Ribosome


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX82
#24: Protein 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A / Ribosome


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX23
#25: Protein 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A / Ribosome


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#26: Protein 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31 / Ribosome


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#27: Protein 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32 / Ribosome


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX41
#29: Protein 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42' /


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#30: Protein 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33 / Ribosome


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05743
#31: Protein 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A / Ribosome


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#32: Protein 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24 /


Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#35: Protein 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28 / Ribosome


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#36: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32 /


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38061
#37: Protein 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37 / Ribosome


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05744
#38: Protein 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A / Ribosome


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#39: Protein 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A / Ribosome


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX84
#40: Protein 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39 / Ribosome


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05745
#41: Protein 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55 / Ribosome


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49166
#42: Protein 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38 /


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#43: Protein 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40 /


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650
#45: Protein 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38 /


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#46: Protein 60S ribosomal protein L1-A / Ribosome / L10a / Large ribosomal subunit protein uL1-A / Ribosome


Mass: 24524.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX43
#47: Protein 60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35 / Ribosome


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX25
#48: Protein 60S ribosomal protein L12-A / Ribosome / L15 / Large ribosomal subunit protein uL11-A / YL23 / Ribosome


Mass: 17850.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX53

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Pre-rRNA-processing protein ... , 3 types, 5 molecules Kw067

#16: Protein Pre-rRNA-processing protein IPI1 / Involved in processing IST2 protein 1


Mass: 37928.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZSZ4
#57: Protein Pre-rRNA-processing protein IPI3 / Involved in processing IST2 protein 3


Mass: 61836.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53877
#58: Protein Pre-rRNA-processing protein RIX1 / Involved in processing IST2 protein 2 / Ribosomal export protein 1


Mass: 86839.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38883

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Ribosome assembly ... , 2 types, 2 molecules Wx

#28: Protein Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P33201
#53: Protein Ribosome assembly protein 4 / Notchless protein homolog 1 / Ribosome biogenesis factor RSA4


Mass: 57106.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25382

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Nucleolar GTP-binding protein ... , 2 types, 2 molecules bm

#33: Protein Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02892
#44: Protein Nucleolar GTP-binding protein 2


Mass: 55585.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53742

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Ribosome biogenesis protein ... , 3 types, 3 molecules cru

#34: Protein Ribosome biogenesis protein ALB1 / /


Mass: 19322.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZQK9
#49: Protein Ribosome biogenesis protein NSA2 / / NOP7-associated protein 2 /


Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZR80
#52: Protein Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like /


Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q07915

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Non-polymers , 3 types, 8 molecules

#59: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#60: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#61: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rix1-Rea1 pre-60S assembly particle - composite structure of the entire particle
Type: RIBOSOME
Details: Rix1-TAP Flag-Rea1 derived pre-60S assembly complex
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 75 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 48 / Used frames/image: 1-48

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Processing

EM software
IDNameVersionCategory
1RELION3.0.8particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7UCSF Chimeramodel fitting
9RELION3.0.8initial Euler assignment
10RELION3.0.8final Euler assignment
11RELION3.0.8classification
12RELION3.0.83D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 273799
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114398
Details: Resolution of the consensus refined map: 3.1A. Resolutions of the individual rigid bodies after Rigid Body Refinement: 3.0A (60S core); 3.3A (Rix1-subcomplex); 4.2A (Rea1 ring and tail)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID3D fitting-ID
16HYP1
26HYD1
36OR51
46QTA1
53JCT1
66N8J1

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