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- PDB-5jcs: CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE -

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Basic information

Entry
Database: PDB / ID: 5jcs
TitleCRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE
Components
  • (60S ribosomal protein ...) x 37
  • (Ribosome assembly ...) x 2
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Eukaryotic translation initiation factor 6
  • Midasin
  • Nucleolar GTP-binding protein 1
  • Probable metalloprotease ARX1
  • Protein SDA1
  • Ribosome biogenesis protein RLP24
KeywordsRIBOSOME / pre-60S ribosome rix1 rea1
Function / homology
Function and homology information


protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / Hydrolases / traversing start control point of mitotic cell cycle / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / Hydrolases / traversing start control point of mitotic cell cycle / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ATPase activator activity / negative regulation of mRNA splicing, via spliceosome / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / ribosomal subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / maturation of LSU-rRNA / translation initiation factor activity / Neutrophil degranulation / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / metallopeptidase activity / rRNA processing / protein transport / ribosome biogenesis / ATPase binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / proteolysis / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SDA1 domain / Midasin / Uncharacterised domain NUC130/133, N-terminal / Sda1 / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / : / SDA1, conserved domain / SDA1, HEAT repeat ...SDA1 domain / Midasin / Uncharacterised domain NUC130/133, N-terminal / Sda1 / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / : / SDA1, conserved domain / SDA1, HEAT repeat / Midasin AAA lid domain / Midasin AAA lid domain / Midasin AAA+ ATPase lid domain / SDA1, C-terminal / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / : / Sigma-54 interaction domain, ATP-binding site 1 / NLE / NLE (NUC135) domain / Ribosome assembly factor Mrt4 / : / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / GTP binding domain / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / metallochaperone-like domain / TRASH domain / VWFA domain profile. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / von Willebrand factor, type A / : / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / : / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL11A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Ribosome assembly protein 4 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL13A / Ribosome assembly factor MRT4 / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Protein SDA1 / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Nucleolar GTP-binding protein 1 / Probable metalloprotease ARX1 / Ribosome biogenesis protein RLP24 / Midasin / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsBarrio-Garcia, C. / Thoms, M. / Flemming, D. / Kater, L. / Berninghausen, O. / Bassler, J. / Beckmann, R. / Hurt, E.
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.
Authors: Clara Barrio-Garcia / Matthias Thoms / Dirk Flemming / Lukas Kater / Otto Berninghausen / Jochen Baßler / Roland Beckmann / Ed Hurt /
Abstract: Ribosome synthesis is catalyzed by ∼200 assembly factors, which facilitate efficient production of mature ribosomes. Here, we determined the cryo-EM structure of a Saccharomyces cerevisiae ...Ribosome synthesis is catalyzed by ∼200 assembly factors, which facilitate efficient production of mature ribosomes. Here, we determined the cryo-EM structure of a Saccharomyces cerevisiae nucleoplasmic pre-60S particle containing the dynein-related 550-kDa Rea1 AAA(+) ATPase and the Rix1 subcomplex. This particle differs from its preceding state, the early Arx1 particle, by two massive structural rearrangements: an ∼180° rotation of the 5S ribonucleoprotein complex and the central protuberance (CP) rRNA helices, and the removal of the 'foot' structure from the 3' end of the 5.8S rRNA. Progression from the Arx1 to the Rix1 particle was blocked by mutational perturbation of the Rix1-Rea1 interaction but not by a dominant-lethal Rea1 AAA(+) ATPase-ring mutant. After remodeling, the Rix1 subcomplex and Rea1 become suitably positioned to sense correct structural maturation of the CP, which allows unidirectional progression toward mature ribosomes.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
SupersessionDec 14, 2016ID: 5FL8
Revision 1.1Dec 14, 2016Group: Other
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: em_image_scans / pdbx_unobs_or_zero_occ_atoms ...em_image_scans / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Jul 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,814,39848
Polymers2,814,39848
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein 60S ribosomal protein L2-A / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL2A, RPL5B, YFR031C-A, YFR031BC / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX45
#2: Protein 60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL30, RPL32, YGL030W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#3: Protein 60S ribosomal protein L3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL3, MAK8, TCM1, YOR063W, YOR29-14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#4: Protein 60S ribosomal protein L31-A / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL31A, RPL34, RPL34A, YDL075W, D2478 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8
#5: Protein 60S ribosomal protein L4-A / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL4A, RPL2, RPL2A, YBR031W, YBR0315 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#6: Protein 60S ribosomal protein L32


Mass: 14809.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL32, YBL092W, YBL0838 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#7: Protein 60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL5, RPL1, RPL1A, YPL131W, LPI14W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#8: Protein 60S ribosomal protein L33-A / L37 / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL33A, RPL37A, YPL143W, LPI4W, P2625 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05744
#9: Protein 60S ribosomal protein L6-A / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL6A, RPL17A, YL16A, YML073C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02326
#10: Protein 60S ribosomal protein L34-A


Mass: 13673.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL34A, YER056C-A, YER056BC / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P87262
#11: Protein 60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL7A, RPL6A, RPL8A, YL8A, YGL076C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#12: Protein 60S ribosomal protein L35-A


Mass: 13942.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL35A, SOS1, YDL191W, D1249 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX84
#13: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL8A, MAK7, RPL4A, YHL033C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#14: Protein 60S ribosomal protein L36-A / L39 / YL39


Mass: 11151.259 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL36A, RPL39A, YMR194W, YM9646.06 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05745
#15: Protein 60S ribosomal protein L9-A / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL9A, RPL8A, RPL9, YGL147C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738
#16: Protein 60S ribosomal protein L37-A / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL37A, RPL35A, YLR185W, L9470.6 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#17: Protein 60S ribosomal protein L1-A / L10a


Mass: 24524.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL1A, SSM1, SSM1A, YPL220W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX43
#18: Protein 60S ribosomal protein L38


Mass: 8845.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL38, YLR325C, L8543.2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49167
#19: Protein 60S ribosomal protein L11-A / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL11A, RP39A, RPL16A, YPR102C, P8283.14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W9
#20: Protein 60S ribosomal protein L39 / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL39, RPL46, SPB2, YJL189W, J0360 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650
#21: Protein 60S ribosomal protein L12-A / L15 / YL23


Mass: 17850.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL12A, RPL15B, YEL054C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX53
#23: Protein 60S ribosomal protein L13-A


Mass: 22604.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL13A, YDL082W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12690
#25: Protein 60S ribosomal protein L14-A


Mass: 15195.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL14A, YKL006W, YKL153 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105
#27: Protein 60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL15A, RPL10A, RPL13A, YL10A, YLR029C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#28: Protein 60S ribosomal protein L43-A / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL43A, YPR043W, YP9499.02 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX25
#29: Protein 60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL16A, RPL13, RPL21A, YIL133C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#31: Protein 60S ribosomal protein L17-A / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL17A, RPL17, RPL20A, YKL180W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#33: Protein 60S ribosomal protein L18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL18A, RP28A, YOL120C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX49
#35: Protein 60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX82
#37: Protein 60S ribosomal protein L20-A / L18a


Mass: 20478.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX23
#39: Protein 60S ribosomal protein L21-A


Mass: 18279.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL21A, URP1, YBR191W, YBR1401 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#41: Protein 60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL22A, YLR061W, L2168 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05749
#43: Protein 60S ribosomal protein L23-A / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX41
#45: Protein 60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL25, YOL127W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#46: Protein 60S ribosomal protein L26-A / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL26A, RPL26, RPL33A, YLR344W, L8300.4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#47: Protein 60S ribosomal protein L27-A


Mass: 15568.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL27A, RPL27, YHR010W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H6
#48: Protein 60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL28, CYH2, YGL103W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406

-
Protein , 6 types, 6 molecules morstu

#22: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TIF6, CDC95, YPR016C, LPZ15C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12522
#26: Protein Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NOG1, YPL093W, LPG15W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02892
#32: Protein Protein SDA1 / Severe depolymerization of actin protein 1


Mass: 86755.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SDA1, YGR245C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53313
#34: Protein Midasin / MIDAS-containing protein / Ribosome export/assembly protein 1


Mass: 559951.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MDN1, REA1, YLR106C, L2901, L8004.13 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12019
#36: Protein Ribosome biogenesis protein RLP24 / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RLP24, YLR009W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q07915
#38: Protein Probable metalloprotease ARX1 / Associated with ribosomal export complex protein 1


Mass: 65290.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ARX1, YDR101C, YD8557.10c / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03862, Hydrolases

-
Ribosome assembly ... , 2 types, 2 molecules nq

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


Mass: 27098.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MRT4, YKL009W, YKL160 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33201
#30: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RSA4, YCR072C, YCR72C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25382

-
RNA chain , 3 types, 3 molecules xyz

#40: RNA chain 25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822
#42: RNA chain 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1036126960
#44: RNA chain 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039022925

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Rix1-Rea1 pre-60S particle / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 15749 / Symmetry type: POINT

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