[English] 日本語
Yorodumi
- PDB-6ylx: pre-60S State NE1 (TAP-Flag-Nop53) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ylx
Titlepre-60S State NE1 (TAP-Flag-Nop53)
Components
  • (60S ribosomal protein ...) x 31
  • (Ribosome biogenesis protein ...) x 5
  • 25S rRNA
  • 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
  • 5.8S rRNA5.8S ribosomal RNA
  • Eukaryotic translation initiation factor 6
  • ITS2Internal transcribed spacer
  • Nuclear GTP-binding protein NUG1
  • Nucleolar GTP-binding protein 1
  • Pescadillo homolog
  • Proteasome-interacting protein CIC1
  • Ribosome assembly factor MRT4
  • UPF0642 protein YBL028C
KeywordsRIBOSOME / pre-60S / Biogenesis / LSU / Large subunit / ribosome assembly
Function / homology
Function and homology information


27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / enzyme-directed rRNA 2'-O-methylation / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / RNA methylation / rRNA primary transcript binding / RNA methyltransferase activity ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / enzyme-directed rRNA 2'-O-methylation / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / RNA methylation / rRNA primary transcript binding / RNA methyltransferase activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / nuclear-transcribed mRNA catabolic process / positive regulation of ATPase activity / ribosomal large subunit binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / ribosomal subunit export from nucleus / ATPase activator activity / 90S preribosome / preribosome, large subunit precursor / ribonucleoprotein complex assembly / rRNA methylation / proteasome binding / negative regulation of mRNA splicing, via spliceosome / regulation of translational fidelity / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / proteasome complex / mature ribosome assembly / maturation of LSU-rRNA / translation initiation factor activity / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / protein catabolic process / protein-macromolecule adaptor activity / rRNA processing / large ribosomal subunit rRNA binding / macroautophagy / cytoplasmic translation / ribosome biogenesis / ribosomal large subunit assembly / cytosolic large ribosomal subunit / ribosome binding / 5S rRNA binding / negative regulation of translation / ribosome / rRNA binding / ATPase binding / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein L30, conserved site / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal RNA methyltransferase FtsJ domain / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L13 / Translation initiation factor IF6 ...Ribosomal protein L30, conserved site / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal RNA methyltransferase FtsJ domain / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L13 / Translation initiation factor IF6 / KOW / Ribosomal protein L24/L26, conserved site / Ribosomal protein L7, eukaryotic / GTP binding domain / Ribosomal protein L34Ae / Translation protein SH3-like domain superfamily / Ribosomal protein L14e domain / Ribosomal protein L38e / Pescadillo / Ribosomal protein L13e / Ribosomal protein L23/L25, conserved site / Ribosomal protein L22/L17 / Ribosomal protein L27e / Ribosomal protein L21e / Ribosomal protein L15, conserved site / BRCT domain / Ribosomal protein L32e / Ribosomal protein L22e / Ribosomal protein L37e / Ribosomal protein L35A / Ribosomal protein L10P / Ribosomal protein L29/L35 / Ribosomal protein L7A/L8 / Ribosomal protein L4/L1e / Ribosomal protein L6, conserved site-2 / Translation protein, beta-barrel domain superfamily / Nucleolar GTP-binding protein 1, Rossman-fold domain / 60S ribosomal protein L6E / Ribosomal protein L37e, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L34e, conserved site / Uncharacterised protein family UPF0642 / 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 / Ribosomal protein L29, conserved site / Ribosomal protein L18e, conserved site / TRASH domain / NOG, C-terminal / Ribosomal protein L37ae/L37e / Zinc-binding ribosomal protein / Ribosome biogenesis protein Nop53/GLTSCR2 / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal RNA methyltransferase, Spb1, C-terminal / Ribosomal protein L30, N-terminal / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L25/L23 / Ribosomal protein L2, domain 2 / Guanine nucleotide-binding protein-like 3, N-terminal domain / Ribosomal RNA large subunit methyltransferase E / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L24e-related / Ribosomal protein L6 / Ribosomal protein L18e/L15P / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / BRCT domain superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L32e superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / RNA-binding domain superfamily / Ribosomal protein L19/L19e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L34Ae superfamily / Ribosome biogenesis protein 15, RNA recognition motif / NOG1, N-terminal helical domain / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L10-like domain superfamily / Ribosomal Protein L6, KOW domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L14, KOW motif
Ribosome assembly factor MRT4 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / UPF0642 protein YBL028C / Proteasome-interacting protein CIC1 / Nuclear GTP-binding protein NUG1 / Ribosome biogenesis protein RLP7 / 60S ribosomal protein L38 / 60S ribosomal protein L37-A / gb:834774822: ...Ribosome assembly factor MRT4 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / UPF0642 protein YBL028C / Proteasome-interacting protein CIC1 / Nuclear GTP-binding protein NUG1 / Ribosome biogenesis protein RLP7 / 60S ribosomal protein L38 / 60S ribosomal protein L37-A / gb:834774822: / Ribosome biogenesis protein 15 / 60S ribosomal protein L34-A / 60S ribosomal protein L6-A / 60S ribosomal protein L21-A / Nucleolar GTP-binding protein 1 / Ribosome biogenesis protein RLP24 / Ribosome biogenesis protein NOP53 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L13-A / 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase / gb:1331532632: / 60S ribosomal protein L16-A / 60S ribosomal protein L27-A / 60S ribosomal protein L8-A / 60S ribosomal protein L33-A / Ribosome biogenesis protein NSA2 / Pescadillo homolog / 60S ribosomal protein L28 / 60S ribosomal protein L25 / 60S ribosomal protein L39 / 60S ribosomal protein L7-A / 60S ribosomal protein L9-A / 60S ribosomal protein L17-A / 60S ribosomal protein L26-A / 60S ribosomal protein L36-A / 60S ribosomal protein L3 / 60S ribosomal protein L15-A / 60S ribosomal protein L22-A / 60S ribosomal protein L31-A / 60S ribosomal protein L20-A / 60S ribosomal protein L23-A / 60S ribosomal protein L18-A / 60S ribosomal protein L19-A / 60S ribosomal protein L35-A / 60S ribosomal protein L4-A / 60S ribosomal protein L30 / gb:1102641490:
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKater, L. / Beckmann, R.
CitationJournal: Mol. Cell / Year: 2020
Title: Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Authors: Lukas Kater / Valentin Mitterer / Matthias Thoms / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering ...Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1-Ipi3 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10841
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4-A
E: 60S ribosomal protein L6-A
F: 60S ribosomal protein L7-A
G: 60S ribosomal protein L8-A
H: 60S ribosomal protein L9-A
K: Proteasome-interacting protein CIC1
L: 60S ribosomal protein L13-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L15-A
O: 60S ribosomal protein L16-A
P: 60S ribosomal protein L17-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
V: 60S ribosomal protein L23-A
W: Ribosome assembly factor MRT4
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28
b: Nucleolar GTP-binding protein 1
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
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
l: 60S ribosomal protein L39
n: Pescadillo homolog
o: Ribosome biogenesis protein 15
q: Ribosome biogenesis protein NOP53
r: Ribosome biogenesis protein NSA2
s: Nuclear GTP-binding protein NUG1
t: Ribosome biogenesis protein RLP7
u: Ribosome biogenesis protein RLP24
y: Eukaryotic translation initiation factor 6
z: UPF0642 protein YBL028C
1: 25S rRNA
2: 5.8S rRNA
6: ITS2
w: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)2,371,22547
Polymers2,371,22547
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
60S ribosomal protein ... , 31 types, 31 molecules BCEFGHLMNOPQRSTUVXYZacdefghijkl

#1: Protein 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1 /


Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14126
#2: Protein 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2 / Ribosome


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10664
#3: Protein 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16 / Ribosome


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02326
#4: Protein 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8 / Ribosome


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05737
#5: Protein 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5 / Ribosome


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#6: Protein 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11 / Ribosome


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05738
#8: Protein 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A / Ribosome


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12690
#9: Protein 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A / Ribosome


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36105
#10: Protein 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18 / Ribosome


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05748
#11: Protein 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15 / Ribosome


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26784
#12: Protein 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17 / Ribosome


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05740
#13: Protein 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28 / Ribosome


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX49
#14: Protein 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14 / Ribosome


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX82
#15: Protein 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A / Ribosome


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX23
#16: Protein 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A / Ribosome


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#17: Protein 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31 / Ribosome


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#18: Protein 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32 / Ribosome


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX41
#20: Protein 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42' /


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#21: Protein 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33 / Ribosome


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05743
#22: Protein 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A / Ribosome


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#23: Protein 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24 /


Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#25: Protein 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38 /


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#26: Protein 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28 / Ribosome


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#27: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32 /


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38061
#28: Protein 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37 / Ribosome


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05744
#29: Protein 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A / Ribosome


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#30: Protein 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A / Ribosome


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX84
#31: Protein 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39 / Ribosome


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05745
#32: Protein 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55 / Ribosome


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49166
#33: Protein 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38 /


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#34: Protein 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40 /


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650

-
Protein , 8 types, 8 molecules KWbnsyzw

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


Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38779
#19: Protein Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P33201
#24: Protein Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02892
#35: Protein Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZV85
#39: Protein Nuclear GTP-binding protein NUG1 / Nuclear GTPase 1


Mass: 57798.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40010
#42: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12522
#43: Protein UPF0642 protein YBL028C


Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38202
#47: Protein 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase / 2'-O-ribose RNA methyltransferase SPB1 / AdoMet-dependent rRNA methyltransferase SPB1 / S-adenosyl- ...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 method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
References: UniProt: P25582, 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase

-
Ribosome biogenesis protein ... , 5 types, 5 molecules oqrtu

#36: Protein Ribosome biogenesis protein 15 / / Nucleolar protein 15 /


Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53927
#37: Protein Ribosome biogenesis protein NOP53 / / Nucleolar protein 53 /


Mass: 52667.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12080
#38: Protein Ribosome biogenesis protein NSA2 / / NOP7-associated protein 2 /


Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZR80
#40: Protein Ribosome biogenesis protein RLP7 / / Ribosomal protein L7-like /


Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40693
#41: Protein Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like /


Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q07915

-
RNA chain , 3 types, 3 molecules 126

#44: RNA chain 25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 834774822
#45: RNA chain 5.8S rRNA / 5.8S ribosomal RNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1331532632
#46: RNA chain ITS2 / Internal transcribed spacer / Internal transcribed spacer


Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1102641490

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: pre-60S assembly state NE1 / Type: RIBOSOME / Details: TAP-Flag-Nop53 derived pre-60S assembly 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
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 300 divisions/in. / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 24 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 2
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-10

-
Processing

EM software
IDNameVersionCategory
1Gautomatchv0.53particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7UCSF Chimeramodel fitting
9RELION3.0.8initial Euler assignment
10RELION3.0.8final Euler assignment
11RELION3.0.8classification
12RELION3.0.83D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 499748
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29163 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID3D fitting-ID
13JCT1
26ELZw1
36N8J1

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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

Read more