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- PDB-6n8j: Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit -

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Entry
Database: PDB / ID: 6n8j
TitleCryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit
Components
  • (60S ribosomal protein ...) x 38
  • (Nucleolar GTP-binding protein ...) x 2
  • (Ribosome biogenesis protein ...) x 2
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Bud site selection protein 20
  • Eukaryotic translation initiation factor 6
  • Ribosome assembly factor MRT4
  • Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
  • UPF0642 protein YBL028C
KeywordsRIBOSOME / ribosome biogenesis / Nmd3 / peptidyl transferase center
Function / homologyNOG1 N-terminal helical domain / Ribosomal biogenesis NSA2 family / Ribosomal protein L22p/L17e / Ribosomal Proteins L2, RNA binding domain / 60S ribosomal protein L10P, insertion domain / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L23 ...NOG1 N-terminal helical domain / Ribosomal biogenesis NSA2 family / Ribosomal protein L22p/L17e / Ribosomal Proteins L2, RNA binding domain / 60S ribosomal protein L10P, insertion domain / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L23 / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L5 / Ribosomal protein L36e domain superfamily / Ribosomal L15 / Ribosomal protein L36e / Ribosomal protein L21e / Ribosomal protein L44 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / ribosomal L5P family C-terminus / Ribosomal protein L3 / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / Ribosomal protein L10 / Ribosomal protein L6 / Ribosomal protein L30p/L7e / Ribosomal protein L38e superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L31e / Ribosomal protein L19/L19e conserved site / P-loop containing nucleoside triphosphate hydrolase / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Nucleolar GTP-binding protein 2 / Nucleolar GTP-binding protein 1 / Ribosomal protein L15e core domain superfamily / Ribosomal protein L39e domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein L31e domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L30, central domain, archaeal type / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L32e superfamily / Zinc finger C2H2 superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein L15 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosome assembly factor Mrt4 / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / OBG-type guanine nucleotide-binding (G) domain / Ribosomal protein L6e / Ribosomal protein L34e / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e signature 1. / Ribosomal protein L13e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein L37e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L1e signature. / Ribosomal protein L13 signature. / Ribosomal protein L6 signature 2. / Ribosomal protein L18e signature. / Ribosomal protein L30 signature. / Ribosomal protein L32e signature. / Ribosomal protein L29 signature. / Ribosomal protein L19e signature. / Ribosomal protein L15 signature. / Ribosomal protein L3 signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L27e signature. / Ribosomal protein L22 signature. / OBG-type guanine nucleotide-binding (G) domain profile. / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L15e signature. / Ribosomal protein L24 signature.
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsZhou, Y. / Musalgaonkar, S. / Johnson, A.W. / Taylor, D.W.
CitationJournal: Nat Commun / Year: 2019
Title: Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.
Authors: Yi Zhou / Sharmishtha Musalgaonkar / Arlen W Johnson / David W Taylor
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 29, 2018 / Release: Mar 13, 2019

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Assembly

Deposited unit
D: 60S ribosomal protein L5
J: 60S ribosomal protein L11-A
A: 60S ribosomal protein L2-A
a: 60S ribosomal protein L28
B: 60S ribosomal protein L3
b: Nucleolar GTP-binding protein 1
C: 60S ribosomal protein L4-A
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31-A
E: 60S ribosomal protein L6-A
e: 60S ribosomal protein L32
F: 60S ribosomal protein L7-A
f: 60S ribosomal protein L33-A
G: 60S ribosomal protein L8-A
g: 60S ribosomal protein L34-A
I: Bud site selection protein 20
H: 60S ribosomal protein L9-A
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
m: Nucleolar GTP-binding protein 2
L: 60S ribosomal protein L13-A
l: 60S ribosomal protein L39
M: 60S ribosomal protein L14-A
p: 60S ribosomal protein L43-A
N: 60S ribosomal protein L15-A
u: Ribosome biogenesis protein RLP24
O: 60S ribosomal protein L16-A
P: 60S ribosomal protein L17-A
Q: 60S ribosomal protein L18-A
R: 60S ribosomal protein L19-A
r: Ribosome biogenesis protein NSA2
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
y: Eukaryotic translation initiation factor 6
Z: 60S ribosomal protein L27-A
z: UPF0642 protein YBL028C
K: 60S ribosomal protein L12
q: 60S ribosomal protein L42-A
o: 60S ribosomal protein L29
1: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
2: 5S rRNA
3: 5.8S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,155,25953
Polyers2,154,16449
Non-polymers1,0954
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)393360
ΔGint (kcal/M)-3060
Surface area (Å2)697410

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Components

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60S ribosomal protein ... , 38 types, 38 molecules DJAaBCcdEeFfGgHhijkLlMpNOPQRST...

#1: Protein/peptide 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: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPL5, RPL1, RPL1A, YPL131W, LPI14W
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain (production host): ATCC 204508 / S288c / References: UniProt: P26321
#2: Protein/peptide 60S ribosomal protein L11-A / Ribosome / L16 / Large ribosomal subunit protein uL5-A / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W9
#3: Protein/peptide 60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#4: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02406
#5: Protein/peptide 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14126
#7: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10664
#8: Protein/peptide 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14120
#9: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12980.158 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H8
#10: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02326
#11: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38061
#12: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05737
#13: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05744
#14: Protein/peptide 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P17076
#15: Protein/peptide 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P87262
#17: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05738
#18: Protein/peptide 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#19: Protein/peptide 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05745
#20: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49166
#21: Protein/peptide 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49167
#23: Protein/peptide 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#24: Protein/peptide 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6358.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04650
#25: Protein/peptide 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36105
#26: Protein/peptide 60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 10112.952 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX25
#27: Protein/peptide 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05748
#29: Protein/peptide 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26784
#30: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05740
#31: Protein/peptide 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#32: Protein/peptide 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#34: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#35: Protein/peptide 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A


Mass: 18279.266 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02753
#36: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05749
#37: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#39: Protein/peptide 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04456
#40: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05743
#42: Protein/peptide 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#44: Protein/peptide 60S ribosomal protein L12 /


Mass: 15951.983 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#45: Protein/peptide 60S ribosomal protein L42-A / Ribosome / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX27
#46: Protein/peptide 60S ribosomal protein L29 / / Large ribosomal subunit protein eL29 / YL43


Mass: 6691.884 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05747

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

#6: Protein/peptide Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02892
#22: Protein/peptide Nucleolar GTP-binding protein 2


Mass: 55585.590 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53742

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Protein/peptide , 4 types, 4 molecules IWyz

#16: Protein/peptide Bud site selection protein 20


Mass: 18546.982 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08004
#38: Protein/peptide Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33201
#41: Protein/peptide Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12522
#43: Protein/peptide UPF0642 protein YBL028C


Mass: 12435.429 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38202

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Ribosome biogenesis protein ... , 2 types, 2 molecules ur

#28: Protein/peptide Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07915
#33: Protein/peptide Ribosome biogenesis protein NSA2 / / NOP7-associated protein 2


Mass: 29786.783 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40078

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RNA chain , 3 types, 3 molecules 123

#47: RNA chain Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA


Mass: 1097493.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: REF: 831416132
#48: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: GenBank: 1329886537
#49: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: GenBank: 1489318609

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Non-polymers , 2 types, 4 molecules

#50: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#51: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium

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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: Late nuclear (LN) pre-60S ribosomal subunit / Type: RIBOSOME
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
Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 20

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
4RELIONCTF correction
7Cootmodel fitting
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 88117 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 3JCT

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