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- EMDB-14001: Specific features and methylation sites of a plant ribosome. 60S ... -

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Basic information

Entry
Database: EMDB / ID: EMD-14001
TitleSpecific features and methylation sites of a plant ribosome. 60S ribosomal subunit.
Map data
Sample
  • Complex: 60S ribosomal subunit
    • Protein or peptide: x 41 types
    • RNA: x 4 types
  • Ligand: x 6 types
KeywordsSolanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA / RIBOSOME
Function / homology
Function and homology information


protein-RNA complex assembly / maturation of LSU-rRNA / cytosolic ribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly ...protein-RNA complex assembly / maturation of LSU-rRNA / cytosolic ribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e 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 L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L35Ae, conserved site / : / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L35 / Ribosomal protein L6e / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L6E / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L14e domain / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L14 / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L35A / Ribosomal protein L35Ae
Similarity search - Domain/homology
Putative 60S ribosomal protein L27a-3-like / Ribosomal protein eL8/eL30/eS12/Gadd45 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 ...Putative 60S ribosomal protein L27a-3-like / Ribosomal protein eL8/eL30/eS12/Gadd45 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 / 60S ribosomal protein L44 / 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 / 60S ribosomal protein L23A / 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 / 60S ribosomal protein L13a / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsCottilli P / Itoh Y / Amunts A
Funding supportEuropean Union, 4 items
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, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14001.png

Downloads & links

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Map

FileDownload / File: emd_14001.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 540 pix.
= 448.2 Å		0.83 Å/pix.
x 540 pix.
= 448.2 Å		0.83 Å/pix.
x 540 pix.
= 448.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0328
Minimum - Maximum-0.310749 - 0.6420937
Average (Standard dev.)-0.00012928087 (±0.01139014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 448.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14001_msk_1.map
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Half map: #2

Fileemd_14001_half_map_1.map
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Half map: #1

Fileemd_14001_half_map_2.map
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Sample components

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Entire : 60S ribosomal subunit

EntireName: 60S ribosomal subunit
Components
  • Complex: 60S ribosomal subunit
    • Protein or peptide: 60S ribosomal protein L8
    • Protein or peptide: Ribos_L4_asso_C domain-containing protein
    • Protein or peptide: Ribosomal protein L3
    • Protein or peptide: Ribosomal_L18_c domain-containing protein
    • Protein or peptide: Ribosomal_L6e_N domain-containing protein
    • Protein or peptide: Thaliana 60S ribosomal protein L7
    • Protein or peptide: Ribosomal_L7Ae domain-containing protein
    • Protein or peptide: 60S ribosomal protein uL6
    • Protein or peptide: 60S ribosomal protein L10
    • Protein or peptide: 60S ribosomal protein uL5
    • Protein or peptide: 60S ribosomal protein L13
    • Protein or peptide: Ribosomal_L14e domain-containing protein
    • Protein or peptide: Ribosomal protein L15
    • Protein or peptide: 60S ribosomal protein uL13
    • Protein or peptide: 50S ribosomal protein L22, chloroplastic
    • Protein or peptide: Ribosomal_L18e/L15P domain-containing protein
    • Protein or peptide: Ribosomal protein L19
    • Protein or peptide: 60S ribosomal protein L18a
    • Protein or peptide: 60S ribosomal protein eL21
    • Protein or peptide: 60S ribosomal protein eL22
    • Protein or peptide: 60S ribosomal protein uL14
    • Protein or peptide: TRASH domain-containing protein
    • Protein or peptide: Ribosomal_L23eN domain-containing protein
    • Protein or peptide: KOW domain-containing protein
    • Protein or peptide: 60S ribosomal protein L27
    • Protein or peptide: Putative 60S ribosomal protein L27a-3-like
    • Protein or peptide: 60S ribosomal protein L29
    • Protein or peptide: Ribosomal_L7Ae domain-containing protein
    • Protein or peptide: 60S ribosomal protein eL31
    • Protein or peptide: 60S ribosomal protein eL32
    • Protein or peptide: 60S ribosomal protein eL33
    • Protein or peptide: 60S ribosomal protein eL34
    • Protein or peptide: Similar to 60S ribosomal protein L35
    • Protein or peptide: 60S ribosomal protein L36
    • Protein or peptide: Ribosomal protein L37
    • Protein or peptide: 60S ribosomal protein L38
    • Protein or peptide: 60S ribosomal protein eL39
    • Protein or peptide: Ubiquitin-like domain-containing protein
    • Protein or peptide: 60S ribosomal protein eL42
    • Protein or peptide: 60S ribosomal protein eL43
    • Protein or peptide: Ribosomal_L28e domain-containing protein
    • RNA: tRNA
    • RNA: 25S rRNA
    • RNA: 5S rRNA
    • RNA: 5.8S rRNA
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: SPERMINE
  • Ligand: SPERMIDINE
  • Ligand: water

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Supramolecule #1: 60S ribosomal subunit

SupramoleculeName: 60S ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#45
Source (natural)Organism: Solanum lycopersicum (tomato)

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Macromolecule #1: 60S ribosomal protein L8

MacromoleculeName: 60S ribosomal protein L8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 28.331898 KDa
SequenceString: MGRVIRAQRK GAGSVFKSHT HHRKGPARFR TLDFGERNGY LKGVITEVIH DPGRGAPLAR VTFRHPFRYK HQKELFVAAE GMYTGQFVY CGKKATLMVG NVLPLRSIPE GAVVCNVEHK VGDRGVFARC SGDYAIVISH NPDNGTTRVK LPSGAKKIVP S GCRAMIGQ ...String:
MGRVIRAQRK GAGSVFKSHT HHRKGPARFR TLDFGERNGY LKGVITEVIH DPGRGAPLAR VTFRHPFRYK HQKELFVAAE GMYTGQFVY CGKKATLMVG NVLPLRSIPE GAVVCNVEHK VGDRGVFARC SGDYAIVISH NPDNGTTRVK LPSGAKKIVP S GCRAMIGQ VAGGGRTEKP MLKAGNAYHK YRVKRNCWPK VRGVAMNPVE HPHGGGNHQH IGHASTVRRD APPGQKVGLI AA RRTGRLR GQARATAAKA DKA

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #2: Ribos_L4_asso_C domain-containing protein

MacromoleculeName: Ribos_L4_asso_C domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 44.852004 KDa
SequenceString: MATAAAIPTT TVQSLENDMA TDSAAVPLPA VMKAPIRPDV VTYVHSNISK NARQPYAVSR KAGHQTSAES WGTGRAVSRI PRVPGGGTH RAGQGAFGNM CRGGRMFAPT QTWRRWHRKI PVNQKRYAVA SAIAASSVPS LVLARGHRIE SVPELPLVVS D SVEGIEKT ...String:
MATAAAIPTT TVQSLENDMA TDSAAVPLPA VMKAPIRPDV VTYVHSNISK NARQPYAVSR KAGHQTSAES WGTGRAVSRI PRVPGGGTH RAGQGAFGNM CRGGRMFAPT QTWRRWHRKI PVNQKRYAVA SAIAASSVPS LVLARGHRIE SVPELPLVVS D SVEGIEKT SNAIKALKQI GAYPDAEKAK DSHAIRPGKG KMRNRRYISR KGPLIVYGTE GAKLVKAFRN IPGVEICHVD RL NLLKLAP GGHLGRFIIW TKCAYEKLDA IYGTFDKPSQ EKKGYLLPRP KMVNADLARI INSDEVQSVV RPIKKDVNKR ATL KKNPLK NLNVLLKLNP YAKTARRMSL LAEAQRVKAK KEKLDKKRHA ITKEEASAIK GASHSWYKTM ISDSDYAEFD NFTK WLGVS Q

UniProtKB: Large ribosomal subunit protein uL4 C-terminal domain-containing protein

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Macromolecule #3: Ribosomal protein L3

MacromoleculeName: Ribosomal protein L3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 44.518234 KDa
SequenceString: MSHRKFEHPR HGSLGFLPRK RAARHRGKVK AFPKDDPSKP CKLTAFLGYK AGMTHIVREV EKPGSKLHKK ETCEAVTIVE TPPMVIVGV VGYVKTPRGL RCLNTVWAQH LSEDIKRRFY KNWCKSKKKA FLKYSKKYET DEGKKDIQAQ LEKLKKYACV I RVLAHTQI ...String:
MSHRKFEHPR HGSLGFLPRK RAARHRGKVK AFPKDDPSKP CKLTAFLGYK AGMTHIVREV EKPGSKLHKK ETCEAVTIVE TPPMVIVGV VGYVKTPRGL RCLNTVWAQH LSEDIKRRFY KNWCKSKKKA FLKYSKKYET DEGKKDIQAQ LEKLKKYACV I RVLAHTQI RKMKGLKQKK AHLMEIQVNG GSIAQKVDFA YGFFEKQVPV DAVFQKDEMI DIIGVTKGKG YEGVVTRWGV TR LPRKT(HIC)R GLRKVACIGA WHPARVSFTV ARAGQNGYHH RTEMNKKVYK LGKVGQESHT ALTEFDRTEK DITPIGGFP HYGVVKEDYL LIKGCCVGTK KRVVTLRQSL LNQTSRVALE EIKLKFIDTS SKFGHGRFQT TQEKQKFYGR LKA

UniProtKB: Ribosomal protein L3

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Macromolecule #4: Ribosomal_L18_c domain-containing protein

MacromoleculeName: Ribosomal_L18_c domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 34.667316 KDa
SequenceString: MAFIKVQKTR AYFKRFQVKF KRRREGKTDY RARNRLINQD KNKYNTPKYR FVVRFTNKDI IAQIVSASIA GDMILASAYA NELPHYGLE VGLTNYAAAY CTGLLLARRV LKKLEMDEEY EGNLEVNGED YSVEPAESRR PFRALLDVGL LRTTTGNRVF G ALKGALDG ...String:
MAFIKVQKTR AYFKRFQVKF KRRREGKTDY RARNRLINQD KNKYNTPKYR FVVRFTNKDI IAQIVSASIA GDMILASAYA NELPHYGLE VGLTNYAAAY CTGLLLARRV LKKLEMDEEY EGNLEVNGED YSVEPAESRR PFRALLDVGL LRTTTGNRVF G ALKGALDG GLDIPHSEKR FAGFSKDSKQ LDADVHRKYI YGGHVATYMQ TLIEDEPEKY QTHFSQYIKK GFEADGLEEM YK KVHAAIR ADPSPKKSEK QPPKQHKRYN LKKLTYEERK AKLIERLNAL NSAAGNDDDD EDDE

UniProtKB: Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein

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Macromolecule #5: Ribosomal_L6e_N domain-containing protein

MacromoleculeName: Ribosomal_L6e_N domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 25.621484 KDa
SequenceString: MAAKKTIRNP ELIRGVGKFS RSKMYHKKGL WAIKKKNGGK LPLHEKKPAV AVAAVKPPKF YPADDVKKPL VNKHKPKPTK LRASITPGT VLIILAGRFK GKRVVFLKQL TSGLLLVTGP FKLNGVPLRR VNQAYVIGTS TKVDVSGVNV EKIDDKYFAK Q VEKKQKKG ...String:
MAAKKTIRNP ELIRGVGKFS RSKMYHKKGL WAIKKKNGGK LPLHEKKPAV AVAAVKPPKF YPADDVKKPL VNKHKPKPTK LRASITPGT VLIILAGRFK GKRVVFLKQL TSGLLLVTGP FKLNGVPLRR VNQAYVIGTS TKVDVSGVNV EKIDDKYFAK Q VEKKQKKG EGEFFEDKKE EKNVLPQEKK DEQKTVDSAL LKAIEGIPEL KAYLSARFSL KSGMKPHELV F

UniProtKB: Large ribosomal subunit protein uL6 N-terminal domain-containing protein

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Macromolecule #6: Thaliana 60S ribosomal protein L7

MacromoleculeName: Thaliana 60S ribosomal protein L7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 28.057986 KDa
SequenceString: MGEGGVVVPE SVLKKQKRNE EWALVKKQEL AVAKKKSVEN RKLIYNRAKQ YAKEYSEQEK ELIRLKREAR LKGGFYVDPE AKLLFIIRI RGINAMPPQT KKILQLLRLR QIFNGVFLKV NKATVNMLHR VEPYVTYGYP NLKSIKELIY KRGYGKVDKQ R IALTDNAV ...String:
MGEGGVVVPE SVLKKQKRNE EWALVKKQEL AVAKKKSVEN RKLIYNRAKQ YAKEYSEQEK ELIRLKREAR LKGGFYVDPE AKLLFIIRI RGINAMPPQT KKILQLLRLR QIFNGVFLKV NKATVNMLHR VEPYVTYGYP NLKSIKELIY KRGYGKVDKQ R IALTDNAV VEQVLGKHGI ICIEDLVHEI ITVGPHFKEA NNFLWPFQLK APLGGLKKKR NHYVEGGDAG NRENFINELI RR MN

UniProtKB: Thaliana 60S ribosomal protein L7

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Macromolecule #7: Ribosomal_L7Ae domain-containing protein

MacromoleculeName: Ribosomal_L7Ae domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 29.362148 KDa
SequenceString: MAPKKGVAVS AKKKPEKAKV LNPLFEKRPK QFGIGGALPP KKDVTRNVRW PRNVTLQRKK RILKMRLKVP PALNQFTKTL DKNLATTLF KMLLKYRPED KAAKKERLVK RAQAEAEGKT PETKKPIIVK YGLKHITYLI EQNKAQLVVI AHDVDPIELV V WLPALCRK ...String:
MAPKKGVAVS AKKKPEKAKV LNPLFEKRPK QFGIGGALPP KKDVTRNVRW PRNVTLQRKK RILKMRLKVP PALNQFTKTL DKNLATTLF KMLLKYRPED KAAKKERLVK RAQAEAEGKT PETKKPIIVK YGLKHITYLI EQNKAQLVVI AHDVDPIELV V WLPALCRK MEIPYCIVKG KARLGSIVHK KTASALCLTT VKNEDKMEFS RVLEAIKANF NDKYEENRKK WGGGIMGSKS QA RTKAKER VLAKEAAQRL N

UniProtKB: Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein

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Macromolecule #8: 60S ribosomal protein uL6

MacromoleculeName: 60S ribosomal protein uL6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 22.004582 KDa
SequenceString: MKTILSSETM DIPDGITIKV KAKQIEVEGP RGKLTRNFKH LNLDFQLIKD EETGKKKLKI DAWFGSRKTT AAIRTALSHV ENLITGVTK GYRYKMRFVY AHFPINASIS GGNKSIEIRN FLGEKKVRKV DMLDGVTVVR SEKVKDELVL DGNDIELVSR S AALINQKC ...String:
MKTILSSETM DIPDGITIKV KAKQIEVEGP RGKLTRNFKH LNLDFQLIKD EETGKKKLKI DAWFGSRKTT AAIRTALSHV ENLITGVTK GYRYKMRFVY AHFPINASIS GGNKSIEIRN FLGEKKVRKV DMLDGVTVVR SEKVKDELVL DGNDIELVSR S AALINQKC HVKNKDIRKF LDGIYVSEKG RIAEEE

UniProtKB: Large ribosomal subunit protein uL6 alpha-beta domain-containing protein

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Macromolecule #9: 60S ribosomal protein L10

MacromoleculeName: 60S ribosomal protein L10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 24.913289 KDa
SequenceString: MGRRPARCYR QIKNKPYPKS RFCRGVPDPK IRIYDVGMKK KGVDEFPFCV HLVSWEKENV SSEALEAARI ACNKYMTKSA GKDAFHLRV RVHPFHVLRI NKMLSCAGAD RLQTGMRGAF GKPQGVCARV AIGQVLLSVR CKDGNANHAQ EALRRAKFKF P GRQKIIVS ...String:
MGRRPARCYR QIKNKPYPKS RFCRGVPDPK IRIYDVGMKK KGVDEFPFCV HLVSWEKENV SSEALEAARI ACNKYMTKSA GKDAFHLRV RVHPFHVLRI NKMLSCAGAD RLQTGMRGAF GKPQGVCARV AIGQVLLSVR CKDGNANHAQ EALRRAKFKF P GRQKIIVS RKWGFTKFSR TDYLKYKSEN RIVPDGVNAK LLGCHGRLAA RQPGRAFLEA AN

UniProtKB: 60S ribosomal protein L10

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Macromolecule #10: 60S ribosomal protein uL5

MacromoleculeName: 60S ribosomal protein uL5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 20.826176 KDa
SequenceString:
MASEKKLSNP MRDIKVQKLV LNISVGESGD RLTRAAKVLE QLSGQSPVFS KARYTVRSFG IRRNEKIACY VTVRGEKAMQ LLESGLKVK EYELLRRNFS ETGCFGFGIQ EHIDLGIKYD PSTGIYGMDF YVVLERPGYR VARRRRCKSR VGIQHRVTKE D SMKWFQVK YEGVILNKSS NIQ

UniProtKB: 60S ribosomal protein L11

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Macromolecule #11: 60S ribosomal protein L13

MacromoleculeName: 60S ribosomal protein L13 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 23.620619 KDa
SequenceString: MKHNNVIPNG HFKKHWQNYV RTWFNQPARK TRRRAARQKK AATIFPRPTA GSLRPIVHGQ TLKYNMKVRA GRGFSLEELK AAGIPKKLA PTIGIAVDHR RRNRSLEGLQ TNVQRLKTYK AKLVIFPRRA KKVKAGDSSA EELANATQVQ GPYLPIVRDQ P AIELVKIT ...String:
MKHNNVIPNG HFKKHWQNYV RTWFNQPARK TRRRAARQKK AATIFPRPTA GSLRPIVHGQ TLKYNMKVRA GRGFSLEELK AAGIPKKLA PTIGIAVDHR RRNRSLEGLQ TNVQRLKTYK AKLVIFPRRA KKVKAGDSSA EELANATQVQ GPYLPIVRDQ P AIELVKIT DEMKSFKAYG KLRIERTNAR HFGARLKRAA EAEKEEKK

UniProtKB: 60S ribosomal protein L13

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Macromolecule #12: Ribosomal_L14e domain-containing protein

MacromoleculeName: Ribosomal_L14e domain-containing protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 15.400435 KDa
SequenceString:
MPFKRFVEIG RVALINYGKD YGRLVVIVDV IDQNRALVDA PDMVRSQMNF KRLSLTDIKI DIKRIPKKKT LVEAMEAADV KTKWENSSW GRKLIVQKRR AALNDFDRFK LMLAKIKRAG VVRQELAKLK KIAA

UniProtKB: Large ribosomal subunit protein eL14 domain-containing protein

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Macromolecule #13: Ribosomal protein L15

MacromoleculeName: Ribosomal protein L15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 24.23327 KDa
SequenceString: MGAYTYVSEL WRKKQSDVMR FLQRVRCWEY RQLPSIVRVT RPTRPDKARR LGYKAKQGYV VYRVRVKRGG RKRPVSKGIV YGKPTNQGV TQLKFQRSKR SVAEERAGRK LGGLKVLNSY WINEDSTYKY FEVILVDQAH AAIRNDPRIN WICNPVHKHR E LRGLTSAG ...String:
MGAYTYVSEL WRKKQSDVMR FLQRVRCWEY RQLPSIVRVT RPTRPDKARR LGYKAKQGYV VYRVRVKRGG RKRPVSKGIV YGKPTNQGV TQLKFQRSKR SVAEERAGRK LGGLKVLNSY WINEDSTYKY FEVILVDQAH AAIRNDPRIN WICNPVHKHR E LRGLTSAG KKYRGLRGRG HLHHKARPSR RATWKRNQTL SLRRYR

UniProtKB: Ribosomal protein L15

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Macromolecule #14: 60S ribosomal protein uL13

MacromoleculeName: 60S ribosomal protein uL13 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 23.613238 KDa
SequenceString: MVSGSGISAR RIVVDARHHM LGRLSSILAK ELLNGQRVVV VRCEEICLSG GLVRQKMKYL RFLRKRMNTK PSHGPIHFRA PSKILWRTI RGMIPHKTKR GAAALARLKV YEGVPPPYDK IKRMVIPDAL KVLRLQSGHK YCLLGKLSSE VGWNHYDTIK E LENKRKER ...String:
MVSGSGISAR RIVVDARHHM LGRLSSILAK ELLNGQRVVV VRCEEICLSG GLVRQKMKYL RFLRKRMNTK PSHGPIHFRA PSKILWRTI RGMIPHKTKR GAAALARLKV YEGVPPPYDK IKRMVIPDAL KVLRLQSGHK YCLLGKLSSE VGWNHYDTIK E LENKRKER AQVAYERRKQ LAKLRVKAEK AAEEKLGPQL AVIEPIKY

UniProtKB: 60S ribosomal protein L13a

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Macromolecule #15: 50S ribosomal protein L22, chloroplastic

MacromoleculeName: 50S ribosomal protein L22, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 19.785711 KDa
SequenceString:
MVKYSREPDN PTKSCKSRGS SLRVHFKNTR ETAHALRKMP LDKAKSYLED VLAHKQAIPF TRFCRGVGRT AQAKNRHSNG QGRWPVKSA GFILDLLKNA ESNAEVKGLD VDSLYISHIQ VNEAQKQRRR TYRAHGRINP YMSHPCHIEL ILSEKEESVK K EPETQLAP RKAKA

UniProtKB: Uncharacterized protein

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Macromolecule #16: Ribosomal_L18e/L15P domain-containing protein

MacromoleculeName: Ribosomal_L18e/L15P domain-containing protein / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 20.764543 KDa
SequenceString:
MGIDLVAGGK SKKTKRTAPK SDDVYLKLLV KLYRFLARRT GSKFNAVILK RLFMSKINKP PLSLSRLITY ATGKGDNIVV LVGTVTDDV RAYEVPKIKV CALKFTETAR ARIEKAGGEC LTFDQLALRA PLGQNTLLLR GPKNSREAVK HFGPAPGVPH S HTKPYVRA KGRKFERARG KRNSRGYKA

UniProtKB: Large ribosomal subunit protein uL15/eL18 domain-containing protein

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Macromolecule #17: Ribosomal protein L19

MacromoleculeName: Ribosomal protein L19 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 24.786572 KDa
SequenceString: MVSLKLQKRL AASVLKCGRG KVWLDPNEGN EISMANSRQN IRKLVKDGFI IRKPTKIHSR SRARRMKEAK RKGRHSGYGK RKGTREARL PTKVLWMRRL RVLRRLLRKY RESKKIDKHM YHDMYMKVKG NVFKNKRVLM ENIHKTKAEK AREKTLSDQF E ARRAKNKA ...String:
MVSLKLQKRL AASVLKCGRG KVWLDPNEGN EISMANSRQN IRKLVKDGFI IRKPTKIHSR SRARRMKEAK RKGRHSGYGK RKGTREARL PTKVLWMRRL RVLRRLLRKY RESKKIDKHM YHDMYMKVKG NVFKNKRVLM ENIHKTKAEK AREKTLSDQF E ARRAKNKA SRERKFARRK KRLAQGPGGE KPVQPAAPAA AAPAQPAQGS KKSKK

UniProtKB: Ribosomal protein L19

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Macromolecule #18: 60S ribosomal protein L18a

MacromoleculeName: 60S ribosomal protein L18a / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 21.476303 KDa
SequenceString:
MVTYKFHQYQ VVGRALPSEN DEHPKIYRMK LWATNEVRAK SKFWYFLRKL KKVKKSNGQM LAINEIFEKY PTTIKNYGIW LRYQSRTGY HNMYKEYRDT TLNGAVEQMY TEMASRHRVR HHCIQIIKTA TIPAKLCKRE STKQFHDSKI KFPLVFKKVR P PSRKLKTT YKATKPNLFM

UniProtKB: 60S ribosomal protein L18a

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Macromolecule #19: 60S ribosomal protein eL21

MacromoleculeName: 60S ribosomal protein eL21 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 18.715795 KDa
SequenceString:
MPAGHGLRSR TRDSFSRAFR KKGTIALSTY LRIFKIGDYV DIKVNGAIHK GMPHKFYHGR TGRVWNVTKR AVGVEVNKQV RNKILRKRI HVRIEHVQQS RCTEEVRERI KKNDQLKADA KARGEVISTK RQPLGPKPGF MVEGATLETV TPIPYDVVND L KGGY

UniProtKB: 60S ribosomal protein L21

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Macromolecule #20: 60S ribosomal protein eL22

MacromoleculeName: 60S ribosomal protein eL22 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 13.996085 KDa
SequenceString:
MSRAAAAVKG GKKKGASFVI DCSKPVEDSI MEIASLDKFL QERIKVGGKA GALGDSVTVT RDKNKITVTC NSTFSKRYLK YLVKKYLKK NNVRDWLRVI ASNKDRNVYE LRYFNIAENE ADEED

UniProtKB: 60S ribosomal protein L22

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Macromolecule #21: 60S ribosomal protein uL14

MacromoleculeName: 60S ribosomal protein uL14 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 15.040856 KDa
SequenceString:
MSKRGRGGSA GNKFRMSLGL PVAATVNCAD NTGAKNLYII SVKGIKGRLN RLPSACVGDM VMATVKKGKP DLRKKVMPAV IVRQRKPWR RKDGVFMYFE DNAGVIVNPK GEMKGSAITG PIGKECADLW PRIASAANAI V

UniProtKB: 60S ribosomal protein L23

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Macromolecule #22: TRASH domain-containing protein

MacromoleculeName: TRASH domain-containing protein / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 18.712115 KDa
SequenceString:
MMVLKTELCR FSGAKIYPGR GIRFIRSDSQ VFLFVNSKCK HYFHNKLKPS KLTWTAMYRK QHKKDIAQEA AKKRRRTTKK PYSRSIVGA TLEVIQKKRT ERPEVRDAAR EAALREIKER IKKTKDEKKA KKAEVQAKSQ KAGGKGNMSK GGASKGPKLG G GGGKR

UniProtKB: TRASH domain-containing protein

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Macromolecule #23: Ribosomal_L23eN domain-containing protein

MacromoleculeName: Ribosomal_L23eN domain-containing protein / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 17.427744 KDa
SequenceString:
MAPAKVDLTK KKDPKAQAVK AAKAVKSGST FKKKSSKIRT KVTFHRPKTL KKDRSPKYPR VSAPGRNRLD QYAILKYPLT TESAMKKIE DNNTLVFIVD IKADKKKIKD AVKKMYDIQI KKVNTLIRPD GTKKAYVRLT PDYDALDVAN KIGII

UniProtKB: 60S ribosomal protein L23A

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Macromolecule #24: KOW domain-containing protein

MacromoleculeName: KOW domain-containing protein / type: protein_or_peptide / ID: 24
Details: MKYNPRVSSSRRKSRKAHFTAPSSLRRVLMSAPLSSELRAKYSVRSMPVRKDDEVQVVRG TYKGREGKVVQVYRKKWVIHIERITREKVNGSTVNVGIHPSKVVISKLRLDKDRRSLLDR KAKGRAAADKDKGTKFTTEEIMQAID
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 16.750533 KDa
SequenceString:
MKYNPRVSSS RRKSRKAHFT APSSVRRVLM SAPLSSELRA KYNVRSMPVR KDDEVQVVRG TYKGREGKVV QVYRKKWVIH IERITREKV NGSTVNVGIN PSKVVVSKLR LDKDRRSLLD RKAKGRAAAD KDKGTKFTTE EIMQAID

UniProtKB: KOW domain-containing protein

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Macromolecule #25: 60S ribosomal protein L27

MacromoleculeName: 60S ribosomal protein L27 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 15.698643 KDa
SequenceString:
MVKFLKPNKA VILLQGKYAG RKAVIVRAFD EGTRDRPYGH CLVAGISKYP KKVIRKDSAK KQAKKSRVKA FIKLVNYNHI MPTRYTLDV DLKDVVNADV LQARDKKVTA AKETKARFEE RFKTGKNRWF FTKLRF

UniProtKB: 60S ribosomal protein L27

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Macromolecule #26: Putative 60S ribosomal protein L27a-3-like

MacromoleculeName: Putative 60S ribosomal protein L27a-3-like / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 16.479389 KDa
SequenceString:
MTTRFKKNRK KRGHVSAGHG RIGKHRKHPG GRGNAGGMHH HRILFDKYHP GYFGKVGMRY FHKLRNKFYC PTVNIDTLWS LVPQEVKDK AAANKGTAPL IDVTQFGYFK VLGKGVLPTG QPVVVKAKLI SKNAEKKIKE NGGAVVLTA

UniProtKB: Putative 60S ribosomal protein L27a-3-like

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Macromolecule #27: 60S ribosomal protein L29

MacromoleculeName: 60S ribosomal protein L29 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 6.989926 KDa
SequenceString:
MAKSKNHTAH NQSYKAHRNG IKKPKSHRHS STKGMDPKFL RNQRYARKHN KKNGETAAEE

UniProtKB: 60S ribosomal protein L29

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Macromolecule #28: Ribosomal_L7Ae domain-containing protein

MacromoleculeName: Ribosomal_L7Ae domain-containing protein / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 12.367472 KDa
SequenceString:
MVAAKKTKKT HESINNRLAL VMKSGKYTLG YKTVLKTIRS SKGKLVIIAN NCPPLRKSEI EYYAMLAKVG VHHYNGNNVD LGTACGKYY RVSCLSIIDP GDSDIIKSLP SDQ

UniProtKB: Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein

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Macromolecule #29: 60S ribosomal protein eL31

MacromoleculeName: 60S ribosomal protein eL31 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 13.890225 KDa
SequenceString:
MVEKTKGRKE EVVSREYTIN LHKRLHGCTF KKKAPTAIKE IRKFAQKAMG TKDVRVDVKL NKQIWSRGIR SVPRRVRVRI ARKRNDDED AKEELYSLVT VAEIPAEGLK GLGTKIIEDE E

UniProtKB: 60S ribosomal protein L31

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Macromolecule #30: 60S ribosomal protein eL32

MacromoleculeName: 60S ribosomal protein eL32 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 15.673507 KDa
SequenceString:
MAVPLLNKKV VKKRVKRFIR PQSDRRITVK ESWRRPKGID SRVRRKFKGC VLMPNIGYGS DKKTRHYLPN GFKKFVVHNA SELEILMMH NRTYCAEIAH NVSTRKRKEI VERAAQLDVV ITNKLARLHS QEDE

UniProtKB: 60S ribosomal protein L32

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Macromolecule #31: 60S ribosomal protein eL33

MacromoleculeName: 60S ribosomal protein eL33 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 12.952167 KDa
SequenceString:
MVKGRQGERI RLYVRGTVLG YKRSKSNQYP NTSLIQIEGV NTKEEVDWYL GKRLGYIYKA KTKKNNSHYR CIWGKVCRPH GNSGVVRAK FKSNLPPKSM GAKVRVFMYP SNI

UniProtKB: 60S ribosomal protein L35a

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Macromolecule #32: 60S ribosomal protein eL34

MacromoleculeName: 60S ribosomal protein eL34 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 13.815384 KDa
SequenceString:
MVQRLTYRKR HSYATKSNQH RVVKTPGGKL IYQTTKKRAN GPKCPVTGKR IQGIPHLRPA EYKRSRLSRN RRTVNRAYGG VLSGSAVRE RIIRAFLVEE QKIVKKVLKI QKAKEKLASK S

UniProtKB: 60S ribosomal protein L34

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Macromolecule #33: Similar to 60S ribosomal protein L35

MacromoleculeName: Similar to 60S ribosomal protein L35 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 14.324415 KDa
SequenceString:
MARIKVHELR NKSKTELLAQ LKDLKAELAL LRVAKVTGGA PNKLSKIKVV RLSIAQVLTV ISQKQKAALR EVYKNKKYLP LDLRPKKTR AIRKRLTKHQ SSLKTEREKK KEMYFPLRKY AIKV

UniProtKB: Similar to 60S ribosomal protein L35

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Macromolecule #34: 60S ribosomal protein L36

MacromoleculeName: 60S ribosomal protein L36 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 12.406898 KDa
SequenceString:
MAPKQPNTGI SVGLNKGHVV TKKELAPRPS DRKGKTSKRI HFVRSLIREV AGFAPYEKRI TELLKVGKDK RALKVAKRKL GTHKRAKKK REEMSSVLRK MRATGGGEKK K

UniProtKB: 60S ribosomal protein L36

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Macromolecule #35: Ribosomal protein L37

MacromoleculeName: Ribosomal protein L37 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 10.809628 KDa
SequenceString:
MGKGTGSFGK RRNKTHTLCV RCGRRSFHLQ KSRCSACAYP AARLRSYNWS VKAIRRKTTG TGRMRYLRNV PRRFKTNFRE GTEAAPRKK GTAASA

UniProtKB: Ribosomal protein L37

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Macromolecule #36: 60S ribosomal protein L38

MacromoleculeName: 60S ribosomal protein L38 / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 8.101704 KDa
SequenceString:
MPKQIHEIKD FLLTARRKDA RTVKIKKNKD MVKFKVRCSK YLYTLCVSDF EKADKLKQSL PPGLSVQDL

UniProtKB: Large ribosomal subunit protein eL38

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Macromolecule #37: 60S ribosomal protein eL39

MacromoleculeName: 60S ribosomal protein eL39 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 6.489813 KDa
SequenceString:
MPSHKSFMIK KKLAKKQRQN RPIPYWIRMR TDNTIRYNAK RRHWRRTKLG F

UniProtKB: 60S ribosomal protein L39

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Macromolecule #38: Ubiquitin-like domain-containing protein

MacromoleculeName: Ubiquitin-like domain-containing protein / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 14.745399 KDa
SequenceString:
MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN IQKESTLHLV LRLRGGIIEP SLMALARKY NQEKMICRKC YARLHPRAVN CRKRKCGHSN QLRPKKKIK

UniProtKB: Ubiquitin-like domain-containing protein

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Macromolecule #39: 60S ribosomal protein eL42

MacromoleculeName: 60S ribosomal protein eL42 / type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 12.037346 KDa
SequenceString:
MVNVPKTKKT YCKSKECKKH TLHKVTQYKK GKDSLAAQGK RRYDRKQSGY GGQTKPVFHK KAKTTKKIVL RLQCQGCKHV SQHPIKRCK HFEIGGDKKG KGTSLF

UniProtKB: 60S ribosomal protein L44

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Macromolecule #40: 60S ribosomal protein eL43

MacromoleculeName: 60S ribosomal protein eL43 / type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 10.280108 KDa
SequenceString:
MTKRTKKAGI VGKYGTRYGA SLRKQIKKME VSQHSKYFCE FCGKYAVKRK AVGIWGCKDC GKVKAGGAYT LNTASAVTVR STIRRLREQ TES

UniProtKB: 60S ribosomal protein L37a

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Macromolecule #41: Ribosomal_L28e domain-containing protein

MacromoleculeName: Ribosomal_L28e domain-containing protein / type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 16.018641 KDa
SequenceString:
M(THC)TVPGQLVW EIVKKNNSFL VKEFGNGTAG VVFSKEPNNL YNLHSYKHSG LANKKTVTIQ PDGKDKSVLL ATSKTK KQN KPSRLLNKSV MKKEFSRMAK AVTNQVGDNY YRPDLKKAAL ARLSAVHRSL KVTKSGAKKR NRQA

UniProtKB: Ribosomal eL28/Mak16 domain-containing protein

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Macromolecule #42: tRNA

MacromoleculeName: tRNA / type: rna / ID: 42 / Number of copies: 1
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 589.43 Da
SequenceString:
CA

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Macromolecule #43: 25S rRNA

MacromoleculeName: 25S rRNA / type: rna / ID: 43 / Number of copies: 1
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 1.098453 MDa
SequenceString: GCGACCCCAG GUCAGGCGGG AUUACCCGCU GAGU(PSU)UAAGC AUA(OMU)CAA(OMU)AA GCGGAGGAAA AGAAACU (PSU)A CAAGGAUUCC CCUAGUAACG GCGAGCGAAC CGGGAACAGC CCAGCCUUAG AAUCGGGCGG CUCCGUCGUC CGAA (OMU)UGUA ...String:
GCGACCCCAG GUCAGGCGGG AUUACCCGCU GAGU(PSU)UAAGC AUA(OMU)CAA(OMU)AA GCGGAGGAAA AGAAACU (PSU)A CAAGGAUUCC CCUAGUAACG GCGAGCGAAC CGGGAACAGC CCAGCCUUAG AAUCGGGCGG CUCCGUCGUC CGAA (OMU)UGUA GUCUGGAGAA GCGUCCUCAG CGGCGGACCG GGCCCAAGUC CCCUGGAAGG GGGCGCCGGA GAGGGUGAGA G CCCCGUCG UGCCCGGACC CUGUCGCACC ACGAGGCGCU GUCUACGAGU CGGGUUGUUU GGGAAUGCAG CCCAAAUCGG GC GGUGAAU UCCGUCCAAG GCUAAAUACU GGCGAGAGAC CGAUAGCGAA CAAGUACCGC GAGGGAAAGA UG(A2M)AAAGGA CU(PSU)UGAAAAG AGAGUCAAAG AGU(OMG)CUUGAA AUUGUCGGGA GGGAAGCGGA UGGGGGCCGG CGAUGCGCCC CG GUCGGAU GUGGAACGGC GACGAGCCGG UCCGCCGAUC GACUCGGGGC GUGGACCAGC GUGGAUUGGG GGGGCGGCCA AAG CCCGGG CUCUCGAUAC GCCCGUGGAA CGCCGUCUCC CCGAUUGUGG AAGGCAGCGC GCGCCUCCGG CGUGCUUCGG CAUC UGCGC GCUCCGGACG CUGGCCUGUG GGCUCCCCAU UCGACCCGUC UUG(1MA)AAC(A2M)CG GACCAAGGAG U(OMC) (OMU)GACAUG UGUGCGAGUC AACGGGCGAG UAAACCCGUA AGGCGUAAGG AAGCUGAUUG GUGGGAUCCC CCUGAGGGG UGCACCGCCG ACCGACCUUG AUCUUCUGAG AAGGGUUCGA GUGUGAGCAU ACC(OMU)GUCGGG ACCC(OMG)A(A2M)A G AUGGUGA(A2M)C(PSU) AUGCCUGAGC GGGGCGAAGC CAGAGGAAAC UCUGGUGGAG GCCCGCAGCG AUACUG(A2M) CG UGCAAA(PSU)CGU UCGUCUGACU UGGGUAUAG(OMG) GGCGAAAGAC UAAUCGAACC GUCUAGU(A2M)GC UGGUUC CCU CCGAAGUUUC CC(PSU)CAGGAUA GCUGGAGCUC GCGUGCGAGU UCUA(PSU)CGGGU AAAGCCAA(PSU)G AUUAG AGGC CUCGGGGGCG CAACGCCCUC GACCUAU(PSU)CU CAAACUU(PSU)AA A(OMU)AGGUAGGA CGGCGCGGCU GCUU UGUUG AGCCGCGCCA CGGAAUCAAG AGCUCCAAGU GGGCCAU(PSU)(PSU)(PSU) UGGUAAGC(A2M)G AACUGGCGA UGCGGGAUGA ACCGGAAGCC GGGUUACGGU GCCAAACUGC GCGCUAACCU AGAUCCCACA AAGGGUGUUG GUCGA(PSU) UAA GACAGCAGGA CGGUGGUCAU GGAAGUCGAA AUCCGCUAAG GAGUGUGUAA CAACUCACCU GCCGAAUCAA CUAGCCC CG AAAAUGGAUG GCGCUUAAGC GCGCGACCUA CACCCGGCCG UCGGGGCAAG UGCCAGGCCC CGAUG(A2M)GUAG GAGG GCGCG GCGGUCGCUG CAAAACCUUG GGCGCGAGCC UGGGCGGAGC GGCCGUCGGU GCAGAU(OMC)UUG GUGGUAGU (A2M) (OMG)CAAAUAUUC AAA(PSU)GAGAA(OMC) U(PSU)UGAAGGCC GAAGAGGGGA AAGGUUCCAU GUGAACGGC ACUUGCACAU GGGUUAG(OMU)CG AUCCUAAGGG UCGGGGGAAC CCCGACAGAU AGCGCGUUUC GCGCGUACUC CGAAAG GGA AUCGGGUUAA AAUUCCUGAA CCGGGACGUG GCGGUUGACG GCAACGUUAG GAAGUCCGGA GACGUCGGCG GGAGCCU CG GGAAGAGUUA UCUUUUCUGU UUAACAGCCU GCCCACCCUG GAAUCGGCUC AGCCGGAGGU AGGGUCCAGC GGCUGGAA G AGCACCGCAC GUCGCGUGGU GUCCGGUGCG CUCCCGGCGG CCCUUGAAAA UCCGGAGGAC CGAAUGCCGU CCACGCCCG GUCGUACUCA UAA(OMC)CG(OMC)AUC A(OMG)GUCU(OMC)CAA GGUGAACAGC CUCUGGUCGA UGGAACAA(OMU)G UAGGCAAGG GAAG(PSU)CGGCA AAAUGGAUCC GUAACUUCGG GAAAAGGAUU GGCUCUGAGG GCUGGGCACG GGGGUCC CA GUCCCGAACC CGUCGGCUGU CGGUGGACUG CUCGAGCUGC UCCCGCGGCG AGAGCGGGUC GCCGCGUGCC GGCCGGGG G ACGGACUGGG AACGGUUCCU UCGGGGGCCU UCCCCGGGCG UCGAACAGCC AACUCAGAAC UGG(OMU)ACGGAC AAG (OMG)(OMG)G(A2M)AU CCGAC(PSU)G(PSU)UU AAUUAAAACA AAGCAUUGCG AUGGUCCCAA CGGAUGUUUA CGCA AUGUG AUU(PSU)CUGCC(OMC) AGUGCUCUGA AUG(PSU)CAAAGU GA(A2M)GAAA(PSU)UC AACCAAGC(OMG)C G GGUAAACG GCGGGAG(PSU)A(A2M) C(PSU)A(PSU)GAC(PSU)C(PSU) CUUAAGGUAG C(5MC)AA(A2M)UGCCU C(OMG)UCAU(OMC)UA AUUAGUGACG CGCAUGAA(PSU)G GA(PSU)UA(A2M)CGAG (A2M)UUCCCACUG U(OMC)C CUGUCU AC(OMU)A(PSU)CCAGC GAAACCACAG (OMC)CAAGGGAAC GGGCUUGGCA GAAUCA(OMG)CGG (OMG)GAA AGAAG ACCCU(OMG)(OMU)UGA GC(PSU)UGAC(OMU)CU AGUCCGAC(PSU)U UGUGAAAUGA CUUGAGAGGU GUAGU AUAA GUGGGAGCCG AAAGGCGAAA GUGAAAUACC ACUACUUUUA ACGUUAUUUU ACUUA(PSU)UCCG UGAAUCGGAA GC GGGGCAC UGCCCCUCUU UUUGGACCCA AGGCUCGCUU CGCGGGCCGA UCCGGGCGGA AGACAUUGUC AGGUGGGGAG UU (PSU)GGCUG(OMG) GGCGGCACAU CUGUUAAAAG (A2M)UAACGCAGG (OMU)(OMG)UCCUAAGA UGAGCUCAAC GAG AACAGA AAU(OMC)UCGUGU GGAACAGAAG GGUAAAAGCU CGU(PSU)UGAU(OMU)C UGAUUUCCAG (OMU)ACGAA (OMU)AC GAACCG(PSU)GAA AGCGUGGCCU AACGAUCCUU UAGACCUUCG GAAUUCGAAG CUA(OMG)A(OMG)GUGU C AGAAAAGU UACCACAG(OMG)G AUAACUGGC(PSU) UGUGGCAGC(OMC) AAGCGU(PSU)CAU AGCGACG(PSU)UG CU UUUUGA(PSU) CCUU(5MC)GAUGU CGG(OMC)(PSU)CU(OMU)CC UAUCAUUG(PSU)G AAGCAGAAUU CACCA (A2M)GUG UU(OMG)GAU(OMU)(OMG)(PSU)U CACCCACCAA UAGGGAACG(PSU) G(A2M)G(OMC)UGGG(UR3)U (PSU)AGA(OMC)CGUC GUGAGACAGG U(PSU)AGUUUUAC CCUACUGA(PSU)G ACAGUGUCGC AAUAGUAAUU CAACC UAGU ACGAGAGGAA CCGUUGAUUC ACACAAUUGG CCAUCGCGCU UGGUUGAAAA GCCAGUGGCG CGAAGCUACC GUGUGC UGG AUUAUGAC(PSU)G AACGCCUCUA AGUCAGAAUC CGGGCUAGAA GCGACGCAUG CGCCCGCCGU CCGCUUGCCG ACC CGCAGU AGGGGCCUUU GGCCCCCAAG GGCACGUGUC GUUGGCUAAG UCGCCGCGAC GGAAGCGUCG CGGUGACCGC CUUG AAGUA CAAUUUCCAU CGAGCGGCGG GUAGAAUCCU UUGCAGACGA C(OMU)UAAAUACG CGACGGGGUA UUGUAAGUGG C AGAGUGGC CUUGCUGCCA CGAUCCACUG AGAUUCAGCC CUUUGUCGCU CCGAUUCGU

GENBANK: GENBANK: OK073662.1

+
Macromolecule #44: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 44 / Number of copies: 1
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 38.634941 KDa
SequenceString:
GGAUGCGAUC AUACCAGCAC UAACGCACCG GAUCCCAUCA GAACUCCGAA GUUAAGCGUG CUUGGGCGAG AGUAGUACUA GGAUGGGUG ACCCCCUGGG AAGUCCUCGU GUUGCAUCCC U

GENBANK: GENBANK: X55697.1

+
Macromolecule #45: 5.8S rRNA

MacromoleculeName: 5.8S rRNA / type: rna / ID: 45 / Number of copies: 1
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 53.173613 KDa
SequenceString:
ACAAACGACU CUCGGCAACG GA(PSU)AUCUCGG CUCUCGCAUC GAUGAAG(A2M)AC GUAGCGAAAU GCGAUACUUG GU GUGAAU(PSU) (OMG)CAGAAUCCC GUGAACCAUC GAGUCUUUGA ACGCAAGUUG CGCCCGAAGC CAUUUGGCCG AGGGC ACGU CUGCCUGGGC GUCACGC

GENBANK: GENBANK: MH573911.1

+
Macromolecule #46: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 46 / Number of copies: 90 / Formula: K
Molecular weightTheoretical: 39.098 Da

+
Macromolecule #47: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 47 / Number of copies: 276 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #48: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 48 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #49: SPERMINE

MacromoleculeName: SPERMINE / type: ligand / ID: 49 / Number of copies: 3 / Formula: SPM
Molecular weightTheoretical: 202.34 Da
Chemical component information

ChemComp-SPM:
SPERMINE

+
Macromolecule #50: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 50 / Number of copies: 1 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE

+
Macromolecule #51: water

MacromoleculeName: water / type: ligand / ID: 51 / Number of copies: 3935 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3883

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 335806
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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