[English] 日本語
Yorodumi
- PDB-6n8l: Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n8l
TitleCryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit
Components
  • (60S ribosomal protein ...) x 37
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • 60S ribosomal export protein NMD3
  • Bud site selection protein 20
  • Eukaryotic translation initiation factor 6
  • Nucleolar GTP-binding protein 1
  • Ribosomal Protein uL1
  • Ribosome assembly factor MRT4
  • Ribosome biogenesis protein RLP24
  • Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
  • UPF0642 protein YBL028C
KeywordsRIBOSOME / ribosome biogenesis / Nmd3 / peptidyl transferase center
Function / homology
Function and homology information


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 / 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 large subunit binding / ribosomal subunit export from nucleus / ATPase activator activity / ribonucleoprotein complex assembly ...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 / 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 large subunit binding / ribosomal subunit export from nucleus / ATPase activator activity / ribonucleoprotein complex assembly / preribosome, large subunit precursor / response to cycloheximide / regulation of translational fidelity / negative regulation of mRNA splicing, via spliceosome / ribosomal large subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA / mature ribosome assembly / translation initiation factor activity / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / cytoplasmic translation / large ribosomal subunit rRNA binding / rRNA processing / macroautophagy / ribosome biogenesis / cytosolic large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / negative regulation of translation / rRNA binding / ribosome / ATPase binding / structural constituent of ribosome / nucleic acid binding / translation / mRNA binding / GTP binding / nucleolus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Protein of unknown function (DUF2423) / Ribosomal protein L22/L17 superfamily / Ribosomal protein L15 / OBG-type guanine nucleotide-binding (G) domain / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosome assembly factor Mrt4 / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily ...Protein of unknown function (DUF2423) / Ribosomal protein L22/L17 superfamily / Ribosomal protein L15 / OBG-type guanine nucleotide-binding (G) domain / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosome assembly factor Mrt4 / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Zinc finger C2H2 superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L6, alpha-beta domain superfamily / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L30/YlxQ / 50S ribosomal protein L30e-like / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L14 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L7Ae/L8/Nhp2 family / 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 L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L2, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L2, conserved site / Zinc finger, double-stranded RNA binding / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L13, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L15e core domain superfamily / Nucleolar GTP-binding protein 1 / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L19 / Ribosomal protein L7/L30 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L31e / Ribosomal protein L14p/L23e / Ribosomal protein L10 / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L23 / Ribosomal protein L23, N-terminal domain / KOW motif / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal L27e protein family / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Nucleolar GTP-binding protein 1 (NOG1) / NOGCT (NUC087) domain / NOG1 N-terminal helical domain / Ribosomal protein L32 / Ribosomal protein L21e / Ribosomal protein L35Ae / Ribosomal protein L34e / Ribosomal L29 protein / Ribosomal protein L36e / Ribosomal protein L37e / Ribosomal L38e protein family / Ribosomal L39 protein / Ribosomal L29e protein family / Ribosomal L37ae protein family / Ribosomal protein L44 / Ribosomal protein L24e / NMD3 family / eIF-6 family / Ribosomal L22e protein family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal export protein Nmd3 / Ribosomal large subunit proteins 60S L5, and 50S L18 / 60S ribosomal protein L10P, insertion domain / NOG1, N-terminal helical domain / Ribosomal protein L14, KOW motif / Ribosomal Protein L26/L24, KOW domain / Eukaryotic Ribosomal Protein L27, KOW domain
60S ribosomal protein L29 / 60S ribosomal protein L36-A / 60S ribosomal protein L33-A / 60S ribosomal protein L26-A / 60S ribosomal protein L17-A / 60S ribosomal protein L9-A / 60S ribosomal protein L15-A / 60S ribosomal protein L7-A / 60S ribosomal protein L39 / 60S ribosomal protein L22-A ...60S ribosomal protein L29 / 60S ribosomal protein L36-A / 60S ribosomal protein L33-A / 60S ribosomal protein L26-A / 60S ribosomal protein L17-A / 60S ribosomal protein L9-A / 60S ribosomal protein L15-A / 60S ribosomal protein L7-A / 60S ribosomal protein L39 / 60S ribosomal protein L22-A / 60S ribosomal protein L25 / 60S ribosomal protein L28 / 60S ribosomal protein L11-A / 60S ribosomal export protein NMD3 / 60S ribosomal protein L43-A / 60S ribosomal protein L27-A / 60S ribosomal protein L32 / 60S ribosomal protein L38 / 60S ribosomal protein L34-A / 60S ribosomal protein L6-A / 60S ribosomal protein L21-A / Nucleolar GTP-binding protein 1 / Ribosome biogenesis protein RLP24 / Bud site selection protein 20 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L13-A / ref:831416132: / gb:1329886537: / gb:1489318609: / UPF0642 protein YBL028C / 60S ribosomal protein L14-A / 60S ribosomal protein L20-A / Ribosome assembly factor MRT4 / 60S ribosomal protein L16-A / 60S ribosomal protein L5 / 60S ribosomal protein L8-A / 60S ribosomal protein L3 / 60S ribosomal protein L30 / 60S ribosomal protein L4-A / 60S ribosomal protein L35-A / 60S ribosomal protein L19-A / 60S ribosomal protein L18-A / 60S ribosomal protein L2-A / 60S ribosomal protein L23-A / 60S ribosomal protein L42-A / 60S ribosomal protein L37-A / 60S ribosomal protein L31-A
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhou, Y. / Musalgaonkar, S. / Johnson, A.W. / Taylor, D.W.
Funding support United States, 5items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR160088 United States
Robert A. Welch FoundationF-1938 United States
Army Research OfficeW911NF-15-0120 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53655 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127127 United States
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 /
Abstract: The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the ...The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0371
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
v: 60S ribosomal export protein NMD3
s: Ribosomal Protein uL1
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
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
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
D: 60S ribosomal protein L5
J: 60S ribosomal protein L11-A
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


Theoretical massNumber of molelcules
Total (without water)2,130,49248
Polymers2,130,49248
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area361920 Å2
ΔGint-2870 kcal/mol
Surface area694340 Å2

-
Components

-
Protein , 8 types, 8 molecules vsbIuWyz

#1: Protein 60S ribosomal export protein NMD3 / Nonsense-mediated mRNA decay protein 3


Mass: 59167.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38861
#2: Protein Ribosomal Protein uL1 /


Mass: 18485.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#6: 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) / Strain: ATCC 204508 / S288c / References: UniProt: Q02892
#16: Protein Bud site selection protein 20


Mass: 18546.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08004
#27: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07915
#36: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33201
#39: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12522
#41: Protein UPF0642 protein YBL028C


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

+
60S ribosomal protein ... , 37 types, 37 molecules AaBCcdEeFfGgHhijkLlMpNOPQRSTUV...

#3: Protein 60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#4: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02406
#5: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14126
#7: Protein 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10664
#8: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14120
#9: Protein 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28


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


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02326
#11: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38061
#12: Protein 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


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


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05744
#14: 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


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


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


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


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


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


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49166
#21: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49167
#22: Protein 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#23: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04650
#24: Protein 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


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


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX25
#26: Protein 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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05748
#28: Protein 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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26784
#29: Protein 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


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


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#31: Protein 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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#32: Protein 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


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


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


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


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#37: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04456
#38: Protein 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


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


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#42: Protein 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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26321
#43: Protein 60S ribosomal protein L11-A / Ribosome / L16 / Large ribosomal subunit protein uL5-A / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W9
#44: Protein 60S ribosomal protein L42-A / Ribosome / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


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


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

-
RNA chain , 3 types, 3 molecules 123

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


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


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


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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Early cytoplasmic-late (ECL) 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
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 %

-
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 / Nominal magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / 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

-
Processing

EM software
IDNameCategory
2Leginonimage acquisition
4RELIONCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42030 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3JCT

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

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