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- PDB-6em5: State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing th... -

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Entry
Database: PDB / ID: 6em5
TitleState D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Components
  • (60S ribosomal protein ...) x 29
  • (Ribosome biogenesis protein ...) x 8
  • 25S rRNA (cytosine(2870)-C(5))-methyltransferase
  • 25S ribosomal RNA
  • 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
  • 5.8S ribosomal RNA
  • 60S ribosome subunit biogenesis protein NIP7
  • ATP-dependent RNA helicase HAS1
  • Eukaryotic translation initiation factor 6
  • Internal Transcribed Spacer 2
  • Nuclear GTP-binding protein NUG1
  • Nucleolar GTP-binding protein 1
  • Nucleolar complex-associated protein 3
  • Nucleolar protein 16
  • Pescadillo homolog
  • Proteasome-interacting protein CIC1
  • Protein MAK16
  • Ribosomal RNA-processing protein 1
  • Ribosome assembly factor MRT4
  • Ribosome production factor 1
  • UPF0642 protein YBL028C
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / Large Subunit Biogenesis Nucleolus
Function/homology27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / AdoMet-dependent rRNA methyltransferase, Spb1 / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / ec:2.1.1.310: / RNA (C5-cytosine) methyltransferase, NOP2 / Nucleolar complex-associated protein 3 / Ribosomal RNA methyltransferase, Spb1, C-terminal / Nucleolar complex-associated protein 3, N-terminal / Noc2p-Noc3p complex / rRNA (guanine) methyltransferase activity ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / AdoMet-dependent rRNA methyltransferase, Spb1 / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / ec:2.1.1.310: / RNA (C5-cytosine) methyltransferase, NOP2 / Nucleolar complex-associated protein 3 / Ribosomal RNA methyltransferase, Spb1, C-terminal / Nucleolar complex-associated protein 3, N-terminal / Noc2p-Noc3p complex / rRNA (guanine) methyltransferase activity / Ribosome biogenesis factor, NIP7 / CCAAT-binding factor / Nucleolar complex-associated protein / Spb1 C-terminal domain / Domain of unknown function (DUF3381) / Ribosome biogenesis factor NIP7-like / WD repeat WDR12/Ytm1 / CBF/Mak21 family / Ribosomal RNA large subunit methyltransferase E / Guanine nucleotide-binding protein-like 3, N-terminal domain / Nop2p / Uncharacterised protein family UPF0642 / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / Ribosomal RNA small subunit methyltransferase F, N-terminal / Uncharacterised protein family (UPF0113) / Eukaryotic rRNA processing / snoRNA release from pre-rRNA / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / Mak16 protein / GTP-binding protein, orthogonal bundle domain superfamily / cell cycle DNA replication / NOL1/NOP2/sun family signature. / Ribosome biogenesis protein Nop16 / WDR74/Nsa1 / maturation of 5.8S rRNA / GNL3L/Grn1 putative GTPase / Protein of unknown function (DUF2423) / Ribosome biogenesis protein BRX1 / Nucleolar, Nop52 / Ribosome assembly factor Mrt4 / NOG, C-terminal / WD repeat BOP1/Erb1 / BOP1, N-terminal domain / Nucleolar GTP-binding protein 1 / Domain of unknown function DUF4217 / Nucleolar GTP-binding protein 1, Rossman-fold domain / Eukaryotic rRNA processing protein EBP2 / Pescadillo / nuclear division / NLE / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Mak16 protein C-terminal region / Ribosome biogenesis protein 15, RNA recognition motif / Ribosome biogenesis protein Nop16 / N-terminal domain of 16S rRNA methyltransferase RsmF / regulation of rRNA processing / SAM-dependent MTase RsmB/NOP-type domain profile. / RNA (C5-cytosine) methyltransferase / BOP1NT (NUC169) domain / SAM-dependent methyltransferase RsmB/NOP2-type / Nucleolar protein,Nop52 / Domain of unknown function (DUF4217) / NOGCT (NUC087) domain / PeBoW complex / Nucleolar GTP-binding protein 1 (NOG1) / Pescadillo N-terminus / rRNA primary transcript binding / NLE (NUC135) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Brix domain / Brix domain profile. / Translation initiation factor IF6 / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / 16S rRNA methyltransferase RsmB/F / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PUA domain superfamily / nuclear pre-replicative complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / actomyosin contractile ring assembly / PUA domain / PUA domain profile. / eIF-6 family / Brix domain / mature ribosome assembly / regulation of cell division / rRNA base methylation / RNA-dependent ATPase activity / ribosomal subunit export from nucleus / Ribosomal L28e/Mak16 / chromosome organization / BRCT domain, a BRCA1 C-terminus domain / nuclear-transcribed mRNA catabolic process / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTP binding domain / Ribosomal L28e protein family / ATPase activator activity
Function and homology information
Specimen sourceSaccharomyces cerevisiae / / yeast /
MethodElectron microscopy (4.3 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsKater, L. / Cheng, J. / Barrio-Garcia, C. / Hurt, E. / Beckmann, R.
CitationJournal: Cell / Year: 2017
Title: Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Authors: Lukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann
Abstract: Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.
Copyright: 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 1, 2017 / Release: Dec 27, 2017

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Structure visualization

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Assembly

Deposited unit
2: 5.8S ribosomal RNA
6: Internal Transcribed Spacer 2
L: 60S ribosomal protein L13-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L15-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
Z: 60S ribosomal protein L27-A
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31-A
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
g: 60S ribosomal protein L34-A
i: 60S ribosomal protein L36-B
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
E: 60S ribosomal protein L6-A
G: 60S ribosomal protein L8-A
O: 60S ribosomal protein L16-A
V: 60S ribosomal protein L23-A
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
h: 60S ribosomal protein L35-A
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4-A
H: 60S ribosomal protein L9-A
A: Ribosome biogenesis protein BRX1
K: Proteasome-interacting protein CIC1
m: Ribosome biogenesis protein ERB1
D: ATP-dependent RNA helicase HAS1
W: Ribosome assembly factor MRT4
l: 60S ribosome subunit biogenesis protein NIP7
b: Nucleolar GTP-binding protein 1
o: Ribosome biogenesis protein 15
n: Pescadillo homolog
r: Ribosome biogenesis protein NSA2
s: Nuclear GTP-binding protein NUG1
t: Ribosome biogenesis protein RLP7
y: Eukaryotic translation initiation factor 6
z: UPF0642 protein YBL028C
p: Ribosome biogenesis protein YTM1
q: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
u: Ribosome biogenesis protein RLP24
v: Nucleolar protein 16
w: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
I: Nucleolar complex-associated protein 3
J: rRNA-processing protein EBP2
x: Ribosome production factor 1
3: Protein MAK16
4: Ribosomal RNA-processing protein 1
5: Ribosome biogenesis protein NSA1
1: 25S ribosomal RNA
F: 60S ribosomal protein L7-A
P: 60S ribosomal protein L17-A


Theoretical massNumber of molelcules
Total (without water)2,928,07157
Polyers2,928,07157
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 261

#1: RNA chain 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: GenBank:1214879358
#2: RNA chain Internal Transcribed Spacer 2


Mass: 74308.391 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: GenBank:1102641490
#55: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: GenBank:834774822

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60S ribosomal protein ... , 29 types, 29 molecules LMNQRSTUZcdefgijkEGOVXYhBCHFP

#3: Protein/peptide 60S ribosomal protein L13-A / / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q12690
#4: Protein/peptide 60S ribosomal protein L14-A / / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P36105
#5: Protein/peptide 60S ribosomal protein L15-A / / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P05748
#6: Protein/peptide 60S ribosomal protein L18-A / / Large ribosomal subunit protein eL18-A / RP28


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


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


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


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


Mass: 13711.359 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P05749
#11: Protein/peptide 60S ribosomal protein L27-A / / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P0C2H6
#12: Protein/peptide 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


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


Mass: 12980.158 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P0C2H8
#14: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P38061
#15: Protein/peptide 60S ribosomal protein L33-A / / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P05744
#16: Protein/peptide 60S ribosomal protein L34-A / / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P87262
#17: Protein/peptide 60S ribosomal protein L36-B / / L39 / Large ribosomal subunit protein eL36-B / YL39


Mass: 11162.285 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:O14455
#18: Protein/peptide 60S ribosomal protein L37-A / / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


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


Mass: 8845.561 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P49167
#20: Protein/peptide 60S ribosomal protein L6-A / / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q02326
#21: Protein/peptide 60S ribosomal protein L8-A / / 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 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P17076
#22: Protein/peptide 60S ribosomal protein L16-A / / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P26784
#23: Protein/peptide 60S ribosomal protein L23-A / / L17a / Large ribosomal subunit protein uL14-A / YL32


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


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


Mass: 14265.784 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P05743
#26: Protein/peptide 60S ribosomal protein L35-A / / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P0CX84
#27: 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 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P14126
#28: Protein/peptide 60S ribosomal protein L4-A / / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P10664
#29: Protein/peptide 60S ribosomal protein L9-A / / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P05738
#56: Protein/peptide 60S ribosomal protein L7-A / / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P05737
#57: Protein/peptide 60S ribosomal protein L17-A / / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P05740

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Ribosome biogenesis protein ... , 8 types, 8 molecules Amortpu5

#30: Protein/peptide Ribosome biogenesis protein BRX1 /


Mass: 33585.414 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q08235
#32: Protein/peptide Ribosome biogenesis protein ERB1 / / Eukaryotic ribosome biogenesis protein 1


Mass: 91830.609 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q04660
#37: Protein/peptide Ribosome biogenesis protein 15 / / Nucleolar protein 15


Mass: 25499.186 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P53927
#39: Protein/peptide Ribosome biogenesis protein NSA2 / / NOP7-associated protein 2


Mass: 29786.783 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P40078
#41: Protein/peptide Ribosome biogenesis protein RLP7 / / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P40693
#44: Protein/peptide Ribosome biogenesis protein YTM1 / / Microtubule-associated protein YTM1


Mass: 51426.637 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q12024
#46: Protein/peptide Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q07915
#54: Protein/peptide Ribosome biogenesis protein NSA1 / / NOP7-associated protein 1


Mass: 51982.457 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P53136

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Protein/peptide , 17 types, 17 molecules KDWlbnsyzqvwIJx34

#31: Protein/peptide Proteasome-interacting protein CIC1 / Core interacting component 1


Mass: 42596.691 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P38779
#33: Protein/peptide ATP-dependent RNA helicase HAS1 / Helicase associated with SET1 protein 1


Mass: 56798.348 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q03532, EC:3.6.4.13 (RNA helicase)
#34: Protein/peptide Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P33201
#35: Protein/peptide 60S ribosome subunit biogenesis protein NIP7 / Nuclear import protein 7


Mass: 20411.699 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q08962
#36: Protein/peptide Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q02892
#38: Protein/peptide Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P53261
#40: Protein/peptide Nuclear GTP-binding protein NUG1 / Nuclear GTPase 1


Mass: 57798.652 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P40010
#42: Protein/peptide Eukaryotic translation initiation factor 6 / eIF-6


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


Mass: 12435.429 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P38202
#45: Protein/peptide 25S rRNA (cytosine(2870)-C(5))-methyltransferase / Nucleolar protein 2


Mass: 69912.164 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P40991, EC:2.1.1.310
#47: Protein/peptide Nucleolar protein 16


Mass: 26954.447 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P40007
#48: Protein/peptide 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase / 2'-O-ribose RNA methyltransferase SPB1 / AdoMet-dependent rRNA methyltransferase SPB1 / S-adenosyl-L-methionine-dependent methyltransferase / Suppressor of PAB1 protein 1


Mass: 96656.172 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P25582, EC:2.1.1.167 (27S pre-rRNA (guanosine2922-2'-O)-methyltransferase)
#49: Protein/peptide Nucleolar complex-associated protein 3


Mass: 75689.008 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:Q07896
#50: Protein/peptide rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 49842.613 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P36049
#51: Protein/peptide Ribosome production factor 1 / Ribosome biogenesis protein RPF1


Mass: 35184.387 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P38805
#52: Protein/peptide Protein MAK16 / Maintenance of killer protein 16


Mass: 35754.605 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P10962
#53: Protein/peptide Ribosomal RNA-processing protein 1


Mass: 33250.531 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt:P35178

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Nsa1-TAP Flag-Ytm1 / Type: RIBOSOME
Details: Pre-60S intermediates purified via Nsa1-TAP Flag-Ytm1
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
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 27 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansSampling size: 14 microns / Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 10 / Used frames/image: 1-6

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Processing

EM software
IDNameVersionCategory
1GautomatchPARTICLE SELECTION
4GctfCTF CORRECTION
10RELION2.0INITIAL EULER ASSIGNMENT
11RELION2.0FINAL EULER ASSIGNMENT
12RELION2.0CLASSIFICATION
13RELION2.0RECONSTRUCTION
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 37251 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingDetails: Backbone model / Ref protocol: RIGID BODY FIT / Ref space: REAL

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