[English] 日本語
Yorodumi
- PDB-7qiw: Specific features and methylation sites of a plant ribosome. 60S ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qiw
TitleSpecific features and methylation sites of a plant ribosome. 60S ribosomal subunit.
Components
  • (60S ribosomal protein ...) x 21
  • (Ribosomal protein ...) x 4
  • (Ribosomal_L7Ae domain-containing ...) x 2
  • 25S rRNA
  • 5.8S rRNA
  • 50S ribosomal protein L22, chloroplastic
  • 5S rRNA
  • KOW domain-containing protein
  • Putative 60S ribosomal protein L27a-3-like
  • Ribos_L4_asso_C domain-containing protein
  • Ribosomal_L14e domain-containing protein
  • Ribosomal_L18_c domain-containing protein
  • Ribosomal_L18e/L15P domain-containing protein
  • Ribosomal_L23eN domain-containing protein
  • Ribosomal_L28e domain-containing protein
  • Ribosomal_L6e_N domain-containing protein
  • Similar to 60S ribosomal protein L35
  • TRASH domain-containing protein
  • Thaliana 60S ribosomal protein L7
  • Ubiquitin-like domain-containing protein
  • tRNA
KeywordsRIBOSOME / Solanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA
Function / homology
Function and homology information


protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / modification-dependent protein catabolic process / large ribosomal subunit / protein tag activity / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding ...protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / modification-dependent protein catabolic process / large ribosomal subunit / protein tag activity / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L30/YlxQ / 60S ribosomal protein L35 / Ribosomal Protein L6, KOW domain / Ribosomal protein L7A/L8 / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / 60S ribosomal protein L6E / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L37ae / Ribosomal protein L7, eukaryotic / Ribosomal protein L31e, conserved site / Ribosomal L37ae protein family / Ribosomal protein L31e signature. / Ribosomal_L19e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L39e / Ribosomal protein L14e domain / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L14 / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site
Similarity search - Domain/homology
: / SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Putative 60S ribosomal protein L27a-3-like / Ribosomal_L7Ae domain-containing protein / 60S ribosomal protein L32 / KOW domain-containing protein / Uncharacterized protein / 60S ribosomal protein L35a / Ribosomal protein L37 / Ribosomal eL28/Mak16 domain-containing protein / 60S ribosomal protein L34 / 60S ribosomal protein L29 / Large ribosomal subunit protein uL6 N-terminal domain-containing protein / Ribosomal protein L19 / 60S ribosomal protein L36 / Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein / 60S ribosomal protein L27 / Uncharacterized protein / Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein / Ribosomal protein L15 / Large ribosomal subunit protein uL4 C-terminal domain-containing protein / Large ribosomal subunit protein uL15/eL18 domain-containing protein / 60S ribosomal protein L22 / 60S ribosomal protein L18a / 60S ribosomal protein L21 / TRASH domain-containing protein / Large ribosomal subunit protein uL23 N-terminal domain-containing protein / Large ribosomal subunit protein eL14 domain-containing protein / 60S ribosomal protein L39 / 60S ribosomal protein L13 / Large ribosomal subunit protein uL6 alpha-beta domain-containing protein / 60S ribosomal protein L31 / Uncharacterized protein / Ubiquitin-like domain-containing protein / 60S ribosomal protein L11 / 60S ribosomal protein L37a / 60S ribosomal protein L23 / Thaliana 60S ribosomal protein L7 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL38 / 60S ribosomal protein L10 / Similar to 60S ribosomal protein L35 / Ribosomal protein L3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsCottilli, P. / Itoh, Y. / Amunts, A.
Funding supportEuropean Union, 4items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107European Union
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080European Union
European Molecular Biology Organization (EMBO)H2020-MSCA-IF-2017European Union
CitationJournal: Plant Commun / Year: 2022
Title: Cryo-EM structure and rRNA modification sites of a plant ribosome.
Authors: Patrick Cottilli / Yuzuru Itoh / Yuko Nobe / Anton S Petrov / Purificación Lisón / Masato Taoka / Alexey Amunts /
Abstract: Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to ...Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.
History
DepositionDec 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: 60S ribosomal protein L8
F: Ribos_L4_asso_C domain-containing protein
E: Ribosomal protein L3
G: Ribosomal_L18_c domain-containing protein
H: Ribosomal_L6e_N domain-containing protein
I: Thaliana 60S ribosomal protein L7
J: Ribosomal_L7Ae domain-containing protein
K: 60S ribosomal protein uL6
L: 60S ribosomal protein L10
M: 60S ribosomal protein uL5
N: 60S ribosomal protein L13
O: Ribosomal_L14e domain-containing protein
P: Ribosomal protein L15
Q: 60S ribosomal protein uL13
R: 50S ribosomal protein L22, chloroplastic
S: Ribosomal_L18e/L15P domain-containing protein
T: Ribosomal protein L19
U: 60S ribosomal protein L18a
V: 60S ribosomal protein eL21
W: 60S ribosomal protein eL22
X: 60S ribosomal protein uL14
Y: TRASH domain-containing protein
Z: Ribosomal_L23eN domain-containing protein
a: KOW domain-containing protein
b: 60S ribosomal protein L27
c: Putative 60S ribosomal protein L27a-3-like
d: 60S ribosomal protein L29
e: Ribosomal_L7Ae domain-containing protein
f: 60S ribosomal protein eL31
g: 60S ribosomal protein eL32
h: 60S ribosomal protein eL33
i: 60S ribosomal protein eL34
j: Similar to 60S ribosomal protein L35
k: 60S ribosomal protein L36
l: Ribosomal protein L37
m: 60S ribosomal protein L38
n: 60S ribosomal protein eL39
o: Ubiquitin-like domain-containing protein
p: 60S ribosomal protein eL42
q: 60S ribosomal protein eL43
r: Ribosomal_L28e domain-containing protein
s: tRNA
2: 25S rRNA
5: 5S rRNA
8: 5.8S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,992,651419
Polymers1,981,41145
Non-polymers11,241374
Water70,8893935
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area476690 Å2
ΔGint-3041 kcal/mol
Surface area585150 Å2

-
Components

+
60S ribosomal protein ... , 21 types, 21 molecules DKLMNQUVWXbdfghikmnpq

#1: Protein 60S ribosomal protein L8 / L2 / Ribosomal protein TL2


Mass: 28331.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: P29766
#8: Protein 60S ribosomal protein uL6


Mass: 22004.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7JDZ0
#9: Protein 60S ribosomal protein L10


Mass: 24913.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: Q3SC85
#10: Protein 60S ribosomal protein uL5


Mass: 20826.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4CG62
#11: Protein 60S ribosomal protein L13


Mass: 23620.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7JCM5
#14: Protein 60S ribosomal protein uL13


Mass: 23613.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A6N2B4A3
#18: Protein 60S ribosomal protein L18a


Mass: 21476.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7IGB1
#19: Protein 60S ribosomal protein eL21


Mass: 18715.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7IJQ0
#20: Protein 60S ribosomal protein eL22


Mass: 13996.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7I7E8
#21: Protein 60S ribosomal protein uL14


Mass: 15040.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4CUW3
#25: Protein 60S ribosomal protein L27


Mass: 15698.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GZ83
#27: Protein 60S ribosomal protein L29


Mass: 6989.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GK12
#29: Protein 60S ribosomal protein eL31


Mass: 13890.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7JRW8
#30: Protein 60S ribosomal protein eL32


Mass: 15673.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7F2B5
#31: Protein 60S ribosomal protein eL33


Mass: 12952.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FPS6
#32: Protein 60S ribosomal protein eL34


Mass: 13815.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GDM4
#34: Protein 60S ribosomal protein L36


Mass: 12406.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GUG2
#36: Protein 60S ribosomal protein L38


Mass: 8101.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: P46291
#37: Protein 60S ribosomal protein eL39


Mass: 6489.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7J415
#39: Protein 60S ribosomal protein eL42


Mass: 12037.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7H1I0
#40: Protein 60S ribosomal protein eL43


Mass: 10280.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4CND1

-
Protein , 14 types, 14 molecules FGHIORSYZacjor

#2: Protein Ribos_L4_asso_C domain-containing protein


Mass: 44852.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HW81
#4: Protein Ribosomal_L18_c domain-containing protein


Mass: 34667.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7H274
#5: Protein Ribosomal_L6e_N domain-containing protein


Mass: 25621.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GMA5
#6: Protein Thaliana 60S ribosomal protein L7


Mass: 28057.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: M1BRF8
#12: Protein Ribosomal_L14e domain-containing protein


Mass: 15400.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7J0J5
#15: Protein 50S ribosomal protein L22, chloroplastic


Mass: 19785.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FNQ5
#16: Protein Ribosomal_L18e/L15P domain-containing protein


Mass: 20764.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7I5W4
#22: Protein TRASH domain-containing protein


Mass: 18712.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7IN69
#23: Protein Ribosomal_L23eN domain-containing protein


Mass: 17427.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7INK3
#24: Protein KOW domain-containing protein


Mass: 16750.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MKYNPRVSSSRRKSRKAHFTAPSSLRRVLMSAPLSSELRAKYSVRSMPVRKDDEVQVVRG TYKGREGKVVQVYRKKWVIHIERITREKVNGSTVNVGIHPSKVVISKLRLDKDRRSLLDR KAKGRAAADKDKGTKFTTEEIMQAID
Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FBC6
#26: Protein Putative 60S ribosomal protein L27a-3-like


Mass: 16479.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A0V0H357
#33: Protein Similar to 60S ribosomal protein L35


Mass: 14324.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: Q53U38
#38: Protein Ubiquitin-like domain-containing protein


Mass: 14745.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4B017
#41: Protein Ribosomal_L28e domain-containing protein


Mass: 16018.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FVJ9

-
Ribosomal protein ... , 4 types, 4 molecules EPTl

#3: Protein Ribosomal protein L3


Mass: 44518.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: Q6SKP4
#13: Protein Ribosomal protein L15


Mass: 24233.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HQH0
#17: Protein Ribosomal protein L19


Mass: 24786.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GQ29
#35: Protein Ribosomal protein L37


Mass: 10809.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FV98

-
Ribosomal L7Ae domain-containing ... , 2 types, 2 molecules Je

#7: Protein Ribosomal_L7Ae domain-containing protein


Mass: 29362.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GV73
#28: Protein Ribosomal_L7Ae domain-containing protein


Mass: 12367.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7E9D6

-
RNA chain , 4 types, 4 molecules s258

#42: RNA chain tRNA


Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato)
#43: RNA chain 25S rRNA


Mass: 1098453.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: GenBank: 2090998066
#44: RNA chain 5S rRNA


Mass: 38634.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: GenBank: 19159
#45: RNA chain 5.8S rRNA


Mass: 53173.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: GenBank: 1418500722

-
Non-polymers , 6 types, 4309 molecules

#46: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 90 / Source method: obtained synthetically / Formula: K
#47: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 276 / Source method: obtained synthetically / Formula: Mg
#48: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#49: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#50: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#51: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3935 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 60S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#45 / Source: NATURAL
Source (natural)Organism: Solanum lycopersicum (tomato)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: (1.19.2_4158:phenix.real_space_refine) / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
10RELION3initial Euler assignment
11RELION3.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335806 / Symmetry type: POINT
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 77.84 Å2 / Biso mean: 13.508 Å2 / Biso min: 0.04 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002132906
ELECTRON MICROSCOPYf_angle_d0.414195711
ELECTRON MICROSCOPYf_chiral_restr0.0324281
ELECTRON MICROSCOPYf_plane_restr0.00313438
ELECTRON MICROSCOPYf_dihedral_angle_d12.23261976

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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