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

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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 / ribosome
Function / homologyRibosomal protein L5, C-terminal / Ribosomal protein L29/L35 superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / 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 L19e signature. / Ribosomal protein L5, N-terminal ...Ribosomal protein L5, C-terminal / Ribosomal protein L29/L35 superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / 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 L19e signature. / Ribosomal protein L5, N-terminal / Ribosome assembly factor Mrt4 / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Creatinase/aminopeptidase-like / Ribosomal L18e/L15P superfamily / 60S ribosomal protein L4, C-terminal domain / WD40-repeat-containing domain superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / von Willebrand factor A-like domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Sda1 / Sigma-54 interaction domain, ATP-binding site 1 / Ribosomal protein L34Ae superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L3, conserved site / 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 L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L2, C-terminal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 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 L1, conserved site / Ribosomal protein L1-like / Ribosomal protein L15e core domain superfamily / Nucleolar GTP-binding protein 1 / Ribosomal protein L22e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal L30 N-terminal domain / Ribosomal L22e protein family / Ribosomal L27e protein family / Ribosomal L37ae protein family / Ribosomal L38e protein family / Ribosomal protein L37e / eIF-6 family / Ribosomal protein L14 / Ribosomal protein L23, N-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / SDA1 / Nucleolar GTP-binding protein 1 (NOG1) / AAA domain (dynein-related subfamily) / NLE (NUC135) domain / Ribosomal protein L32 / NOGCT (NUC087) domain / NUC130/3NT domain / Ribosomal L18 C-terminal region / 60S ribosomal protein L4 C-terminal domain / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein 60S L18 and 50S L18e / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L39e signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13e
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.5 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 15, 2016 / Release: Nov 16, 2016
RevisionDateData content typeGroupProviderType
1.0Nov 16, 2016Structure modelrepositoryInitial release
1.1Dec 14, 2016Structure modelOther
1.2May 3, 2017Structure modelDatabase references

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Structure visualization

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  • Deposited structure unit
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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
Polyers2,814,39848
Non-polymers00
Water0
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/peptide 60S ribosomal protein L2-A / Ribosome / L5 / RP8 / YL6


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


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


Mass: 43850.793 Da / Num. of mol.: 1
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 (baker's yeast) / References: UniProt: P14126
#4: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / YL28


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 19755.691 Da / Num. of mol.: 1
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 (baker's yeast) / References: UniProt: P0C0W9
#20: Protein/peptide 60S ribosomal protein L39 / / L46 / YL40


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


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


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


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


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


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


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


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


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


Mass: 21762.316 Da / Num. of mol.: 1
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 (baker's yeast) / References: UniProt: P0CX82
#37: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a


Mass: 20478.852 Da / Num. of mol.: 1
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 (baker's yeast) / References: UniProt: P0CX23
#39: Protein/peptide 60S ribosomal protein L21-A / Ribosome


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


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


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


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


Mass: 14265.784 Da / Num. of mol.: 1
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 (baker's yeast) / References: UniProt: P05743
#47: Protein/peptide 60S ribosomal protein L27-A / Ribosome


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


Mass: 16761.666 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL28, CYH2, YGL103W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406

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Protein/peptide , 6 types, 6 molecules morstu

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


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


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


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


Mass: 559951.438 Da / Num. of mol.: 1
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 (baker's yeast) / References: UniProt: Q12019
#36: Protein/peptide Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like


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


Mass: 65290.336 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ARX1, YDR101C, YD8557.10c / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03862, hydrolases

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

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


Mass: 27098.012 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MRT4, YKL009W, YKL160 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P33201
#30: Protein/peptide Ribosome assembly protein 4 / Notchless protein homolog 1 / Ribosome biogenesis factor RSA4


Mass: 57106.781 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RSA4, YCR072C, YCR72C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25382

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RNA chain , 3 types, 3 molecules xyz

#40: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 834774822
#42: RNA chain 5.8S ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1036126960
#44: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1039022925

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Experimental details

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Experiment

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

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Sample preparation

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

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)

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Processing

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

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