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- PDB-7qiz: Specific features and methylation sites of a plant 80S ribosome -

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Entry
Database: PDB / ID: 7qiz
TitleSpecific features and methylation sites of a plant 80S ribosome
Components
  • (40S body ribosomal protein ...) x 2
  • (40S ribosomal protein ...) x 20
  • (60S ribosomal protein ...) x 22
  • (Ribosomal protein ...) x 5
  • (Ribosomal_L18e/L15P domain-containing ...) x 2
  • 18S
  • 25S rRNA
  • 30S ribosomal protein S15, chloroplasticRibosome
  • 5.8S rRNA5.8S ribosomal RNA
  • 50S ribosomal protein L22, chloroplasticRibosome
  • 5S rRNA5S ribosomal RNA
  • KH type-2 domain-containing protein
  • KOW domain-containing protein
  • Mitogen-activated protein kinase
  • Pectinesterase
  • Ribos_L4_asso_C domain-containing protein
  • Ribosomal_L14e domain-containing protein
  • Ribosomal_L18_c domain-containing protein
  • Ribosomal_L23eN domain-containing protein
  • Ribosomal_L28e domain-containing protein
  • Ribosomal_L6e_N domain-containing protein
  • Ribosomal_L7Ae domain-containing protein
  • Ribosomal_S10 domain-containing protein
  • Ribosomal_S17_N domain-containing protein
  • Ribosomal_S7 domain-containing protein
  • S10_plectin domain-containing protein
  • S5 DRBM domain-containing protein
  • Similar to 60S ribosomal protein L35
  • TRASH domain-containing protein
  • Thaliana 60S ribosomal protein L7
  • Ubiquitin
  • mRNAMessenger RNA
  • tRNATransfer RNA
  • tRNA_1
KeywordsRIBOSOME / Solanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA
Function / homology
Function and homology information


pectinesterase / pectinesterase activity / aspartyl esterase activity / cell wall modification / pectin catabolic process / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / MAP kinase activity ...pectinesterase / pectinesterase activity / aspartyl esterase activity / cell wall modification / pectin catabolic process / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / MAP kinase activity / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / small-subunit processome / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / intracellular signal transduction / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SPARK domain / SPARK / Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Pectin lyase fold ...SPARK domain / SPARK / Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Pectin lyase fold / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L41 / Ribosomal protein L41 / : / Pectin lyase fold/virulence factor / Small (40S) ribosomal subunit Asc1/RACK1 / metallochaperone-like domain / TRASH domain / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / Ribosomal protein L29e / Ribosomal protein S26e / Ribosomal protein S26e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S25 / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L10e / S25 ribosomal protein / Ribosomal protein S21e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S30 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8e, conserved site / Ribosomal protein L24e, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein L34e, conserved site / Ribosomal protein S7e / Ribosomal protein S4e, N-terminal, conserved site / 40S ribosomal protein S4, C-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal S17 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein L23/L25, N-terminal / Ribosomal L38e protein family / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L22e protein family / Ribosomal protein S17, archaeal/eukaryotic / 40S Ribosomal protein S10 / 60S ribosomal protein L35 / Ribosomal protein S27 / Ribosomal protein L35Ae, conserved site / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S3Ae / Plectin/S10, N-terminal / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal L27e protein family
Similarity search - Domain/homology
beta-D-glucopyranose / : / 1,4-DIAMINOBUTANE / SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) ...beta-D-glucopyranose / : / 1,4-DIAMINOBUTANE / SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S30 / 40S ribosomal protein S15a-1 / 40S ribosomal protein S27 / Small ribosomal subunit protein uS10 domain-containing protein / 60S ribosomal protein L32 / 40S ribosomal protein S25 / 40S ribosomal protein S15 / KOW domain-containing protein / 40S ribosomal protein S18 / Uncharacterized protein / Uncharacterized protein / 60S ribosomal protein L35a / 40S ribosomal protein S19 / Ribosomal protein L37 / Ribosomal eL28/Mak16 domain-containing protein / S5 DRBM domain-containing protein / 40S ribosomal protein S21 / 40S ribosomal protein S16 / 60S ribosomal protein L34 / 60S ribosomal protein L29 / Large ribosomal subunit protein uL6 N-terminal domain-containing protein / Ribosomal protein L19 / 40S ribosomal protein S4 / 40S ribosomal protein S26 / 60S ribosomal protein L36 / Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein / Protein kinase domain-containing protein / Ribosomal_L18e/L15P domain-containing protein / 60S ribosomal protein L27 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein / KH type-2 domain-containing protein / Pectinesterase / 40S ribosomal protein S8 / Ribosomal protein L15 / 40S ribosomal protein S6 / Large ribosomal subunit protein uL4 C-terminal domain-containing protein / 40S ribosomal protein S24 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / 60S ribosomal protein L22 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L18a / 60S ribosomal protein L21 / TRASH domain-containing protein / Large ribosomal subunit protein uL23 N-terminal domain-containing protein / Uncharacterized protein / Small ribosomal subunit protein uS7 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 / Plectin/eS10 N-terminal domain-containing protein / Uncharacterized protein / Ubiquitin-like domain-containing protein / 40S ribosomal protein S28 / 60S ribosomal protein L41 / Small ribosomal subunit protein uS17 N-terminal domain-containing protein / 60S ribosomal protein L11 / 60S ribosomal protein L37a / 60S ribosomal protein L23 / Small ribosomal subunit protein uS15 N-terminal domain-containing protein / 30S ribosomal protein S12, chloroplastic / Thaliana 60S ribosomal protein L7 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS17 / Ribosomal protein S14 / 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: 2.38 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 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: Pectinesterase
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: Ribosomal_L18e/L15P domain-containing protein
d: 60S ribosomal protein L29
e: 60S ribosomal protein eL30
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
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
S2: 18S
NA: KH type-2 domain-containing protein
OA: Ribosomal_S7 domain-containing protein
PA: S10_plectin domain-containing protein
QA: 40S ribosomal protein uS19
RA: 40S ribosomal protein uS9
TA: 40S ribosomal protein uS13
UA: 40S ribosomal protein eS19
VA: Ribosomal_S10 domain-containing protein
WA: 40S ribosomal protein eS28
XA: 40S ribosomal protein uS14
YA: Mitogen-activated protein kinase
ZA: 40S ribosomal protein S25
aA: tRNA_1
bA: mRNA
t: 60S ribosomal protein L41
u: 40S ribosomal protein SA
v: 40S ribosomal protein S3a
w: 40S ribosomal protein S4
x: 40S ribosomal protein S7
y: 40S ribosomal protein S8
z: Ribosomal_S17_N domain-containing protein
AA: 40S ribosomal protein S17
BA: 40S ribosomal protein S21
CA: 40S body ribosomal protein uS12
DA: 40S ribosomal protein S26
EA: S5 DRBM domain-containing protein
FA: 40S ribosomal protein S6
GA: 40S body ribosomal protein uS4
HA: 30S ribosomal protein S15, chloroplastic
IA: Ribosomal protein S14
KA: 40S ribosomal protein S24
LA: 40S ribosomal protein S27
MA: 40S ribosomal protein S30
JA: 40S ribosomal protein S15a-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,177,262575
Polymers3,162,34980
Non-polymers14,913495
Water85,1754728
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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60S ribosomal protein ... , 22 types, 22 molecules DKLMNUVWXbdefghikmnpqt

#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
#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
#28: Protein 60S ribosomal protein eL30 /


Mass: 12367.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato)
#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: A0A3Q7FPL2
#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
#61: Protein/peptide 60S ribosomal protein L41 /


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4C3A4

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Protein , 22 types, 22 molecules FGHIJOQRYZajorNAOAPAVAYAzEAHA

#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
#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
#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
#14: Protein Pectinesterase /


Mass: 23613.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HGG4, pectinesterase
#15: Protein 50S ribosomal protein L22, chloroplastic / Ribosome


Mass: 19785.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FNQ5
#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 / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FBC6
#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 /


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
#47: Protein KH type-2 domain-containing protein


Mass: 26828.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HBR5
#48: Protein Ribosomal_S7 domain-containing protein


Mass: 23686.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7IVL4
#49: Protein S10_plectin domain-containing protein


Mass: 19882.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7JYM3
#54: Protein Ribosomal_S10 domain-containing protein


Mass: 13735.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7EMX2
#57: Protein Mitogen-activated protein kinase /


Mass: 35993.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato)
References: UniProt: A0A3Q7GX91, mitogen-activated protein kinase
#67: Protein Ribosomal_S17_N domain-containing protein


Mass: 17740.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4C998
#72: Protein S5 DRBM domain-containing protein


Mass: 30630.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7G7F0
#75: Protein 30S ribosomal protein S15, chloroplastic / Ribosome


Mass: 17099.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4CYU9

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Ribosomal protein ... , 5 types, 5 molecules EPTlIA

#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
#76: Protein Ribosomal protein S14 / / Ribosomal protein S14-like


Mass: 16389.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: Q38JI8

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Ribosomal L18e/L15P domain-containing ... , 2 types, 2 molecules Sc

#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
#26: Protein Ribosomal_L18e/L15P domain-containing protein


Mass: 16479.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GZ10

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RNA chain , 7 types, 7 molecules s258S2aAbA

#42: RNA chain tRNA / Transfer RNA


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 / 5S ribosomal RNA


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 / 5.8S ribosomal RNA


Mass: 53173.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: GenBank: 1418500722
#46: RNA chain 18S


Mass: 583609.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato)
#59: RNA chain tRNA_1


Mass: 4470.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato)
#60: RNA chain mRNA / Messenger RNA


Mass: 895.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato)

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40S ribosomal protein ... , 20 types, 20 molecules QARATAUAWAXAZAuvwxyAABADAFAKALAMAJA

#50: Protein 40S ribosomal protein uS19 /


Mass: 17352.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7F5X2
#51: Protein 40S ribosomal protein uS9 /


Mass: 16805.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GDB0
#52: Protein 40S ribosomal protein uS13 /


Mass: 17574.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FJL7
#53: Protein 40S ribosomal protein eS19 /


Mass: 16056.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FTS1
#55: Protein 40S ribosomal protein eS28 /


Mass: 7551.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4B4Z0
#56: Protein 40S ribosomal protein uS14 /


Mass: 6455.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7ITW7
#58: Protein 40S ribosomal protein S25 /


Mass: 11995.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7F3F2
#62: Protein 40S ribosomal protein SA /


Mass: 32216.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7H1U4
#63: Protein 40S ribosomal protein S3a /


Mass: 29741.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7I881
#64: Protein 40S ribosomal protein S4 /


Mass: 29959.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GQU3
#65: Protein 40S ribosomal protein S7 /


Mass: 22088.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7H0E8
#66: Protein 40S ribosomal protein S8 /


Mass: 24918.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HJ03
#68: Protein 40S ribosomal protein S17 /


Mass: 16265.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: P49215
#69: Protein 40S ribosomal protein S21 /


Mass: 9163.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7G7P4
#71: Protein 40S ribosomal protein S26 /


Mass: 14608.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GRY8
#73: Protein 40S ribosomal protein S6 /


Mass: 28384.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HSH1
#77: Protein 40S ribosomal protein S24 /


Mass: 15445.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7I5D6
#78: Protein 40S ribosomal protein S27 /


Mass: 9620.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A1U8DQX3
#79: Protein 40S ribosomal protein S30 /


Mass: 6953.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A0V0GRY5
#80: Protein 40S ribosomal protein S15a-1 / Ribosome / 40S ribosomal protein S15a-1 isoform X1


Mass: 14551.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A1U7YEG5

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40S body ribosomal protein ... , 2 types, 2 molecules CAGA

#70: Protein 40S body ribosomal protein uS12


Mass: 15771.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4D3L7
#74: Protein 40S body ribosomal protein uS4


Mass: 23051.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4ATQ2

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Sugars , 1 types, 1 molecules

#87: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 5222 molecules

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


Mass: 39.098 Da / Num. of mol.: 119 / Source method: obtained synthetically / Formula: K
#82: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 364 / Source method: obtained synthetically / Formula: Mg
#83: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#84: Chemical ChemComp-SPM / SPERMINE / Spermine


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


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#86: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / Putrescine


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2
#88: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4728 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 80S ribosomeEukaryotic ribosome / Type: RIBOSOME / Entity ID: #1-#80 / 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

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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 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)

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Processing

EM software
IDNameVersionCategory
4GctfCTF correction
10RELION3initial Euler assignment
11RELION3.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335806 / Symmetry type: POINT

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