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- PDB-6elz: State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway o... -

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Entry
Database: PDB / ID: 6elz
TitleState E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosmes
Components
  • (60S ribosomal protein ...) x 30
  • (Ribosome biogenesis protein ...) x 7
  • 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 16Nucleolus
  • Pescadillo homolog
  • Proteasome-interacting protein CIC1
  • Ribosome assembly factor MRT4
  • UPF0642 protein YBL028C
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / Large Subunit Biogenesis Nucleolus
Function / homologyNucleoporin Nup120/160 / Ribosomal protein L38e superfamily / Ribosomal biogenesis NSA2 family / Ribosomal protein L30/YlxQ / 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 ...Nucleoporin Nup120/160 / Ribosomal protein L38e superfamily / Ribosomal biogenesis NSA2 family / Ribosomal protein L30/YlxQ / 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 L36e domain superfamily / Ribosomal protein L22p/L17e / PUA domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / BRCT domain superfamily / Ribosomal protein L22/L17 superfamily / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein L14p/L23e / WD40-repeat-containing domain superfamily / Ribosomal protein L1p/L10e family / Ribosomal protein L31e / 16S rRNA methyltransferase RsmB/F / Ribosomal protein L6e / Ribosomal protein L36e / Ribosomal protein L21e / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / Ribosomal protein L4/L1 family / DEAD/DEAH box helicase / Ribosomal protein L13 / KOW motif / Ribosomal protein L10 / WD domain, G-beta repeat / Ribosomal protein L6 / Ribosomal protein L30p/L7e / Ribosomal protein L3 / Ribosomal protein L23 / Helicase conserved C-terminal domain / Ribosomal protein L32e superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein S8e / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L1-like / Ribosomal protein L19/L19e conserved site / Ribosomal protein L31e domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / RNA (C5-cytosine) methyltransferase, NOP2 / RNA (C5-cytosine) methyltransferase / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L15e core domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L18e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L15e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L31e, conserved site / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / Nucleolar GTP-binding protein 1 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L15 / RNA-binding domain superfamily / Ribosomal protein L19/L19e superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosome biogenesis protein 15, RNA recognition motif / Ribosomal protein L19, eukaryotic / Ribosome assembly factor Mrt4 / Ribosomal RNA small subunit methyltransferase F, N-terminal / OBG-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Domain of unknown function DUF4217 / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / WD repeat WDR12/Ytm1 / WD repeat BOP1/Erb1 / AdoMet-dependent rRNA methyltransferase, Spb1 / P-loop containing nucleoside triphosphate hydrolase / Ribosome biogenesis protein BRX1 / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L34e / Ribosomal protein L24e / Ribosomal protein L14P, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L21e signature. / Ribosomal protein L6e signature. / NOL1/NOP2/sun family signature. / Ribosomal protein L34e signature. / Ribosomal protein L31e signature. / Ribosomal protein L24 signature. / Ribosomal protein L27e signature. / Ribosomal protein L18e signature.
Function and homology information
Specimen sourceSaccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 30, 2017 / Release: Dec 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 27, 2017Structure modelrepositoryInitial release
1.1Feb 7, 2018Structure modelSource and taxonomy / Structure summaryentity / entity_name_com / entity_src_nat_entity.pdbx_description / _entity_src_nat.common_name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain

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Structure visualization

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Assembly

Deposited unit
1: 25S ribosomal RNA
2: 5.8S ribosomal RNA
6: Internal transcribed spacer 2
L: 60S ribosomal protein L13-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-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
O: 60S ribosomal protein L16-A
V: 60S ribosomal protein L23-A
a: 60S ribosomal protein L28
P: 60S ribosomal protein L17-A
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
h: 60S ribosomal protein L35-A
F: 60S ribosomal protein L7-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
E: 60S ribosomal protein L6-A
G: 60S ribosomal protein L8-A
M: 60S ribosomal protein L14-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,788,71555
Polyers2,788,64954
Non-polymers651
Water0
1


  • idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)383080
ΔGint (kcal/M)-2717
Surface area (Å2)721450
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules 126

#1: RNA chain 25S ribosomal RNA / / RDN25-1


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 834774822
#2: RNA chain 5.8S ribosomal RNA / / RDN581-1


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 1214879358
#3: RNA chain Internal transcribed spacer 2 / / ITS2-1


Mass: 74308.391 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 1102641490

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60S ribosomal protein ... , 30 types, 30 molecules LNQRSTUZcdefgijkOVaPXYhFBCHEGM

#4: 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 S288c (yeast) / References: UniProt: Q12690
#5: 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 S288c (yeast) / References: UniProt: P05748
#6: 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 S288c (yeast) / References: UniProt: P0CX49
#7: 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 S288c (yeast) / References: UniProt: P0CX82
#8: 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 S288c (yeast) / References: UniProt: P0CX23
#9: 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 S288c (yeast) / References: UniProt: Q02753
#10: 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 S288c (yeast) / References: UniProt: P05749
#11: 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 S288c (yeast) / 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 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P14120
#13: 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 S288c (yeast) / References: UniProt: P0C2H8
#14: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38061
#15: 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 S288c (yeast) / References: UniProt: P05744
#16: 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 S288c (yeast) / References: UniProt: P87262
#17: 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 S288c (yeast) / References: UniProt: P05745
#18: 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 S288c (yeast) / References: UniProt: P49166
#19: Protein/peptide 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P49167
#20: 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 S288c (yeast) / References: UniProt: P26784
#21: 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 S288c (yeast) / References: UniProt: P0CX41
#22: 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 S288c (yeast) / References: UniProt: P02406
#23: 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 S288c (yeast) / References: UniProt: P05740
#24: 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 S288c (yeast) / References: UniProt: P04456
#25: 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 S288c (yeast) / References: UniProt: P05743
#26: 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 S288c (yeast) / References: UniProt: P0CX84
#27: 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 S288c (yeast) / References: UniProt: P05737
#28: 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 S288c (yeast) / References: UniProt: P14126
#29: 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 S288c (yeast) / References: UniProt: P10664
#30: 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 S288c (yeast) / References: UniProt: P05738
#52: 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 S288c (yeast) / References: UniProt: Q02326
#53: 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 S288c (yeast) / References: UniProt: P17076
#54: 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 S288c (yeast) / References: UniProt: P36105

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Ribosome biogenesis protein ... , 7 types, 7 molecules Amortpu

#31: Protein/peptide Ribosome biogenesis protein BRX1 /


Mass: 33585.414 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q08235
#33: Protein/peptide Ribosome biogenesis protein ERB1 / / Eukaryotic ribosome biogenesis protein 1


Mass: 91830.609 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q04660
#38: Protein/peptide Ribosome biogenesis protein 15 / / Nucleolar protein 15


Mass: 25499.186 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P53927
#40: Protein/peptide Ribosome biogenesis protein NSA2 / / NOP7-associated protein 2


Mass: 29786.783 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: A6ZR80
#42: Protein/peptide Ribosome biogenesis protein RLP7 / / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P40693
#45: Protein/peptide Ribosome biogenesis protein YTM1 / / Microtubule-associated protein YTM1


Mass: 51426.637 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: A6ZPA9
#47: Protein/peptide Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q07915

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Protein/peptide , 14 types, 14 molecules KDWlbnsyzqvwIJ

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


Mass: 42596.691 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38779
#34: Protein/peptide ATP-dependent RNA helicase HAS1 / Helicase associated with SET1 protein 1


Mass: 56798.348 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q03532, RNA helicase
#35: Protein/peptide Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P33201
#36: Protein/peptide 60S ribosome subunit biogenesis protein NIP7 / Nuclear import protein 7


Mass: 20411.699 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q08962
#37: Protein/peptide Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q02892
#39: Protein/peptide Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: A6ZV85
#41: Protein/peptide Nuclear GTP-binding protein NUG1 / Nuclear GTPase 1


Mass: 57798.652 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P40010
#43: Protein/peptide Eukaryotic translation initiation factor 6 / eIF-6


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


Mass: 12435.429 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38202
#46: Protein/peptide 25S rRNA (cytosine(2870)-C(5))-methyltransferase / Nucleolar protein 2


Mass: 69912.164 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P40991, EC: 2.1.1.310
#48: Protein/peptide Nucleolar protein 16 / Nucleolus


Mass: 26954.447 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P40007
#49: 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 / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
References: UniProt: P25582, 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase
#50: Protein/peptide Nucleolar complex-associated protein 3


Mass: 75689.008 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q07896
#51: Protein/peptide rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 49842.613 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P36049

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Non-polymers , 1 types, 1 molecules

#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc

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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: TAP-Flag-Ytm1 E80A / Type: RIBOSOME
Details: Pre-60S ribosomal biogenesis intermediates purified via TAP-Flag-Ytm1 E80A
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
Source: NATURAL
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 27 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansSampling size: 14 microns / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-10

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
4GctfCTF correction
9REFMACmodel refinement
10RELIONinitial Euler assignment
11RELION2.0final Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: NONE
Particle selectionNumber of particles selected: 503000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 112099 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Target criteria: AVERAGE FSC

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  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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