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- EMDB-14002: Specific features and methylation sites of a plant ribosome. 40S ... -

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Basic information

Entry
Database: EMDB / ID: EMD-14002
TitleSpecific features and methylation sites of a plant ribosome. 40S body ribosomal subunit.
Map data
Sample
  • Complex: 40S body ribosomal subunit
    • RNA: x 1 types
    • Protein or peptide: x 21 types
  • Ligand: x 4 types
KeywordsSolanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA / RIBOSOME
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / metal ion binding / cytosol
Similarity search - Function
: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / Ribosomal protein S5, eukaryotic/archaeal ...: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L19, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / : / Ribosomal protein S30 / Ribosomal protein S7e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / Ribosomal protein S6, eukaryotic / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 60S ribosomal protein L19 / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile.
Similarity search - Domain/homology
40S ribosomal protein S30 / 40S ribosomal protein S15a-1 / 40S ribosomal protein S27 / S5 DRBM domain-containing protein / 40S ribosomal protein S21 / Ribosomal protein L19 / 40S ribosomal protein S26 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S8 ...40S ribosomal protein S30 / 40S ribosomal protein S15a-1 / 40S ribosomal protein S27 / S5 DRBM domain-containing protein / 40S ribosomal protein S21 / Ribosomal protein L19 / 40S ribosomal protein S26 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S8 / 40S ribosomal protein S6 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS1 / Uncharacterized protein / 60S ribosomal protein L41 / Small ribosomal subunit protein uS17 N-terminal domain-containing protein / Small ribosomal subunit protein uS15 N-terminal domain-containing protein / 30S ribosomal protein S12, chloroplastic / Small ribosomal subunit protein eS17 / Ribosomal protein S14
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 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) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14002.png

Downloads & links

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Map

FileDownload / File: emd_14002.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
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: 0.0316
Minimum - Maximum-0.20487916 - 0.4392152
Average (Standard dev.)-0.0007611457 (±0.005607971)
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_14002_msk_1.map
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Half map: #1

Fileemd_14002_half_map_1.map
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Half map: #2

Fileemd_14002_half_map_2.map
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Sample components

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Entire : 40S body ribosomal subunit

EntireName: 40S body ribosomal subunit
Components
  • Complex: 40S body ribosomal subunit
    • RNA: 18S rRNA body
    • Protein or peptide: 60S ribosomal protein L41
    • Protein or peptide: 40S ribosomal protein SA
    • Protein or peptide: 40S ribosomal protein S3a
    • Protein or peptide: 40S body ribosomal protein eS4
    • Protein or peptide: 40S ribosomal protein S7
    • Protein or peptide: 40S ribosomal protein S8
    • Protein or peptide: Ribosomal_S17_N domain-containing protein
    • Protein or peptide: 40S ribosomal protein S17
    • Protein or peptide: 40S ribosomal protein S21
    • Protein or peptide: 40S body ribosomal protein uS12
    • Protein or peptide: 40S ribosomal protein S26
    • Protein or peptide: S5 DRBM domain-containing protein
    • Protein or peptide: 40S ribosomal protein S6
    • Protein or peptide: 40S body ribosomal protein uS4
    • Protein or peptide: 30S ribosomal protein S15, chloroplastic
    • Protein or peptide: Ribosomal protein S14
    • Protein or peptide: 40S ribosomal protein S24
    • Protein or peptide: 40S ribosomal protein S27
    • Protein or peptide: 40S ribosomal protein S30
    • Protein or peptide: 40S ribosomal protein S15a-1
    • Protein or peptide: Ribosomal protein L19
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: 40S body ribosomal subunit

SupramoleculeName: 40S body ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Solanum lycopersicum (tomato)

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Macromolecule #1: 18S rRNA body

MacromoleculeName: 18S rRNA body / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 583.16075 KDa
SequenceString: UACCUGGUUG AUCCUGCCAG UAGUCAU(A2M)UG CUUGUCU(OMC)AA AGAUUAAGCC AUGCAUGUGU AAGUAUGAAC AA AUUCAGA CUGUGAAACU GCGAAUGGCU CAU(PSU)AAAUCA G(PSU)UAUAGUUU G(PSU)U(OMU)GAUGGU AUCUACU AC U(OMC) ...String:
UACCUGGUUG AUCCUGCCAG UAGUCAU(A2M)UG CUUGUCU(OMC)AA AGAUUAAGCC AUGCAUGUGU AAGUAUGAAC AA AUUCAGA CUGUGAAACU GCGAAUGGCU CAU(PSU)AAAUCA G(PSU)UAUAGUUU G(PSU)U(OMU)GAUGGU AUCUACU AC U(OMC)GGAUAACC GUAGUAAUUC UAG(A2M)GCUAAU ACGUGCAACA AACCCCGACU UCUGGAAGGG AUGCAUUUA (PSU)UAGAUAAAA GGUCGACGCG GGCUCUGCCC GUUGCUGC(OMG)A UGAUUCA(PSU)GA (PSU)AACUCGACG GAUC GCACG GCCAUCGUGC CGGCGACGCA UCA(PSU)UCAAA(PSU) UUCUGCCCUA UCAACUUUCG AUGGUAGGAU AGUGGCC UA CCAUGGUGGU GACGGG(PSU)GAC GGAGAAUUAG GGUUCGA(PSU)UC CGGAGA(OMG)GGA GCCUGAGAAA CGGCUA CCA CAU(OMC)CAAGGA AGGCAGCAGG CGCGC(A2M)AAUU ACCCAA(PSU)CCU GACACGGGGA GGU(A2M)GUGA (OMC) AAUAAAUAAC AAUACCGGGC UCUAUGAGUC UGGUAAUUGG AAUGAGUACA AUCUAAAUCC CUUAACGAGG (A2M) UCCAUUGG AGGGCAAGUC UGGUGCCAGC AGCCGCGG(OMU)A A(PSU)UCCAGCUC CAAUA(OMG)CGUA (UY1)(UY1) A(PSU)UUAAG UUG(OMU)UGCAGU U(A2M)AAAAGCUC GUAG(PSU)UGGAC UUUGGGAUGG GCCGGCCGGU CCGCCCU AG GUGUGCACCG GUCGUCUCGU CCCUUCUGUC GGCGAUGCGC UCCUGGCCUU AAUUGGCCGG GUCGUGCCUC CGGCGCUG U UACU(PSU)UGAAG AAA(PSU)UAGAGU GCUCAAAGCA AGCCUACGCU CUGUAUACAU U(A2M)GCAUGGGA (PSU)AA CAUUAU AGGAUUUCGG UCCUAUUACG UUGGCCUUCG GGAUCGGAGU AAUGAUUAAC AGGGACAGUC GGGGGCAUUC GUAU UUCAU AGUCAGAGGU GAAAU(PSU)CUUG GAUUUAUGAA AGACGAACAA CUGCGAAAGC AU(PSU)(PSU)GCCAAG GAU GUUUUC AUUAAUCAAG A(A2M)CGAAAGUU GGGGGCUCGA AGACGA(PSU)CAG AUACCG(OMU)CCU AGUCUCAACC A (PSU)AAACGAU GCCGACCAGG GAUCGGCGGA UGUUGCUUUU AGGACUCCGC CGGCACCUUA UGAGAAAUCA AAGUUUUU G GG(PSU)UCCGGGG GGAGUA(PSU)GGU CGCAAGGCUG AAACUUAAAG GAAUUGACGG AAGGGCACCA CCAGGAGUGG A GCC(PSU)GCGG C(PSU)UAAUU(PSU)GA CCAACACGGG GAAACU(PSU)ACC AGG(PSU)(OMC)CAGAC AUAGUAAG G AUUGACAGAC UGAGAGCUCU UUCUUGAUUC (OMU)A(OMU)GGGUGG(OMU) G(OMG)UGCAUGGC GUUCUUAGU (PSU)GGUGGAGCG A(PSU)UUG(PSU)CUGG (PSU)UAAUUCCGU UAACGA(A2M)CGA GACCUCAGCC UGCUAACUAG CUAUGCGGA GGUAUCCCUU CGCGGCCAGC U(OMU)CUUAGAGG GACUACGGCC UUUUAGGCCG CGGAAGUUUG AGGCAAU AA CA(OMG)GUCUGUG AUGCCC(OMU)UAG AUGUUCUGGG CCGCACGCGC GCUACACUGA UGUA(PSU)UCAAC GAGCUU AUA GCCUUGGCCG ACAGGCCCGG GUAAUCUUUG AAAUU(PSU)CA(PSU)C GUGAUGGGGA UAGAUCAUUG CAAUUGU (PSU)G GUCUUCAACG (A2M)G(7MG)AAUUCCU AGUAAGCGCG AGUCAUCAGC UCGCGUUGAC UACGUCCCUG CCCUU (PSU)GUA CACACCG(OMC)CC GUCGCUCCUA CCGAUUGAAU GAUCCGGUGA AAUGUUCGGA UCGCGGCGAC GUGGGCGG U UCGCUGCCCG CGACGUCGCG AGAAGUCCAU UGAACCUUAU CAUUUAGAGG A(A2M)GGAGAAGU CGUA(6MZ)CAAGG U UUC(4AC)GUAG GUG(MA6)(MA6)CCUGC GGAAGGAUCA UUG

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Macromolecule #2: 60S ribosomal protein L41

MacromoleculeName: 60S ribosomal protein L41 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 3.445437 KDa
SequenceString:
MRAKWKKKRM RRLKRKRRKM RQRSK

UniProtKB: 60S ribosomal protein L41

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Macromolecule #3: 40S ribosomal protein SA

MacromoleculeName: 40S ribosomal protein SA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 32.21625 KDa
SequenceString: MATQDVRTLS TKEADIQMML AAEVHLGTKN CDFQMERYAF KRRNDGIYII NLGKTWEKLQ MAARVIVAIE NPQDIIVQSA RPYGQRAVL KFAQYTGAHA IAGRHTPGTF TNQLQTSYSE PRLLILTDPR TDHQPIKEAA LGNIPTIAFC DTDSPMRYVD I GIPANNKG ...String:
MATQDVRTLS TKEADIQMML AAEVHLGTKN CDFQMERYAF KRRNDGIYII NLGKTWEKLQ MAARVIVAIE NPQDIIVQSA RPYGQRAVL KFAQYTGAHA IAGRHTPGTF TNQLQTSYSE PRLLILTDPR TDHQPIKEAA LGNIPTIAFC DTDSPMRYVD I GIPANNKG KHSIGVLFWI LARMVLQMRG AINQGPKWDV MVDLFFYREP EEAKEQEEEV PAIADYADYS ASAALGGDWT SS QIPEAQW TADAAAPAVG GGWAGDGAAD GGWDAAAAPA PVPLPVPDVA PTSGATGWE

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #4: 40S ribosomal protein S3a

MacromoleculeName: 40S ribosomal protein S3a / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 29.741465 KDa
SequenceString: MAVGKNKRIS KGKKGGKKKA ADPYAKKDWY DIKAPSVFEV RNVGKTLVTR TQGTKIASEG LKHRVFEVSL ADLQNDEDHS FRKIRLRAE DVQGRNVLTN FHGMDFTTDK LRSLVKKWQS LIEAHVDVKT TDSYTLRMFC IAFTKKRPNQ QKRTCYAQSS Q IRQIRRKM ...String:
MAVGKNKRIS KGKKGGKKKA ADPYAKKDWY DIKAPSVFEV RNVGKTLVTR TQGTKIASEG LKHRVFEVSL ADLQNDEDHS FRKIRLRAE DVQGRNVLTN FHGMDFTTDK LRSLVKKWQS LIEAHVDVKT TDSYTLRMFC IAFTKKRPNQ QKRTCYAQSS Q IRQIRRKM VEIMRNQAQS CDLKDLVLKF IPESIGREIE KATSSIFPLQ NVFIRKVKIL KAPKFDLGRL MEVHGDYSED VG VKVDRPA EDIATEPTEV VGA

UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #5: 40S body ribosomal protein eS4

MacromoleculeName: 40S body ribosomal protein eS4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 29.95915 KDa
SequenceString: MARGLKKHLK RLNAPKHWML DKLGGAFAPK PSSGPHKSRE CLPLVIILRN RLKYALTYRE VISILMQRQV MVDGKVRTDK TYPAGFMDV VTIPKTNESF RLLYDTKGRF RLHSLRDEEA KFKLCKVRSV QFGQKGIPYL NTYDGRTIRY PDPLIKANDT I KLDLDSNK ...String:
MARGLKKHLK RLNAPKHWML DKLGGAFAPK PSSGPHKSRE CLPLVIILRN RLKYALTYRE VISILMQRQV MVDGKVRTDK TYPAGFMDV VTIPKTNESF RLLYDTKGRF RLHSLRDEEA KFKLCKVRSV QFGQKGIPYL NTYDGRTIRY PDPLIKANDT I KLDLDSNK IVDFIKFDVG NVVMVTGGRN RGRVGILKNR EKHKGSFETV HIQDSQGHEF ATRLGNVFTL GKGSKPWVSL PK GKGIKLS IIEEARKRMA AQSATPA

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Macromolecule #6: 40S ribosomal protein S7

MacromoleculeName: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 22.088475 KDa
SequenceString:
MYTSKQKIHK DKAAEPSEHE VSVGQAFFDL ENTNQELKSE LKDLYINSAT QIDVSGNRKA VVIHVPYRLR KAFRKVHVRL VRELEKKFS GKDVIFIATR RIVRPPKRGS AAQRPRTRTL TSVHDAILED LVVPAEIVGK RTRYRVDGSK IMKVYLDPKE R NNTEYKLE TFSAVYRKLS GKDVVFEYPI TEA

UniProtKB: 40S ribosomal protein S7

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Macromolecule #7: 40S ribosomal protein S8

MacromoleculeName: 40S ribosomal protein S8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 24.918656 KDa
SequenceString: MGISRDSMHK RRATGGKKKS WRKKRKYELG RQPANTKISS NKTVRRIRVR GGNVKWRALR LDTGNFSWGS EAVTRKTRIL DVVYNASNN ELVRTQTLVK SAIVQVDAAP FKQWYLQHYG IDIGRKKKGA AKKETTTEEG DAAEEAKKSN HVVRKIENRQ A DRKLDSHL ...String:
MGISRDSMHK RRATGGKKKS WRKKRKYELG RQPANTKISS NKTVRRIRVR GGNVKWRALR LDTGNFSWGS EAVTRKTRIL DVVYNASNN ELVRTQTLVK SAIVQVDAAP FKQWYLQHYG IDIGRKKKGA AKKETTTEEG DAAEEAKKSN HVVRKIENRQ A DRKLDSHL EEQFASGRLL ACISSRPGQC GRADGYILEG KELEFYMKKL QKKKGKASGA SA

UniProtKB: 40S ribosomal protein S8

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Macromolecule #8: Ribosomal_S17_N domain-containing protein

MacromoleculeName: Ribosomal_S17_N domain-containing protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 17.740814 KDa
SequenceString:
MAEQTEKAFL KQPGVFLSSK KTGKGKRPGK GGNRYFKSIG LGFKTPREAT EGTYIDKKCP FTGNVSIRGR ILAGTCHSAK MNRTIIVRR NYLHYVKKYQ RYEKRHSNIP AHISPCFRVK EGDHVTIGQC RPLSKTVRFN VLKVIPAGSG GVGKKAFTGM

UniProtKB: Small ribosomal subunit protein uS17 N-terminal domain-containing protein

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Macromolecule #9: 40S ribosomal protein S17

MacromoleculeName: 40S ribosomal protein S17 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 16.265969 KDa
SequenceString:
MGRVRTKTVK KSSRQVIERY YSKMTLDFHT NKKILEEVAI IPSKRLRNKI AGFSTHLMKR IQKGPVRGIS LKLQEEERER RMDFVPEES AIKTDLIEVD KETLDMLSAL GMSDLPGVVK QAAEPQAVAA LPSYGRGGGG FGRKY

UniProtKB: Small ribosomal subunit protein eS17

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Macromolecule #10: 40S ribosomal protein S21

MacromoleculeName: 40S ribosomal protein S21 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 9.163203 KDa
SequenceString:
MQNDEGQNMD LYIPRKCSAT NRLITSKDHA SVQLNVGHLD ESGVYTGQFT TYALCGFIRA QGDADSAMDR LWQKKKAEVG QQ

UniProtKB: 40S ribosomal protein S21

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Macromolecule #11: 40S body ribosomal protein uS12

MacromoleculeName: 40S body ribosomal protein uS12 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 15.771567 KDa
SequenceString:
MGKTRGMGAG RKLKSHRRRQ RWADKSYKKS HLGNEWKKPF AGSSHAKGIV LEKIGIEAKQ PNSAIRKCAR VQLIKNGKKI AAFVPNDGC LNYIEENDEV LIAGFGRKGH AVGDIPGVRF KVVKVSGVSL LALFKEKKEK PRS

UniProtKB: 30S ribosomal protein S12, chloroplastic

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Macromolecule #12: 40S ribosomal protein S26

MacromoleculeName: 40S ribosomal protein S26 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 14.608212 KDa
SequenceString:
MTFKRRNGGR NKHGRGHVKF IRCSNCGKCC PKDKAIKRFL VRNIVEQAAV RDVQEACAFE LYTLPKLYLK MQYCVSCAIH SKVVRVRSR TDRRVREPPQ RFRRPRDDLP KTGQAPRPAG GPPAAPRT

UniProtKB: 40S ribosomal protein S26

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Macromolecule #13: S5 DRBM domain-containing protein

MacromoleculeName: S5 DRBM domain-containing protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 30.630678 KDa
SequenceString: MAERGAGDRG GFGRGFGGRG GRGGDRGGRG RGGRRPRRET EEEKWVPVTK LGRLVKDGKI RSLEQIYLHS LPIKEFQIID TLIGPSLKD EVMKIMPVQK QTRAGQRTRF KAFVVVGDGN GHVGLGVKCS KEVATAIRGG IILAKLSVIP VRRGYWGNKI G KPHTVPCK ...String:
MAERGAGDRG GFGRGFGGRG GRGGDRGGRG RGGRRPRRET EEEKWVPVTK LGRLVKDGKI RSLEQIYLHS LPIKEFQIID TLIGPSLKD EVMKIMPVQK QTRAGQRTRF KAFVVVGDGN GHVGLGVKCS KEVATAIRGG IILAKLSVIP VRRGYWGNKI G KPHTVPCK VTGKCGSVTV RMVPAPRGAG IVAARVPKKV LQFAGIEDVF TSSRGSTKTL GNFVKATFDC LMKTYGFLTP DF WKETRFT KSPFQEYFDI LAKPANKVIV YATEEAAPER VEA

UniProtKB: S5 DRBM domain-containing protein

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Macromolecule #14: 40S ribosomal protein S6

MacromoleculeName: 40S ribosomal protein S6 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 28.38423 KDa
SequenceString: MKFNIANPTT GCQKKLEIDD DQKLRAFFDK RISQEVSGDS LGEEFKGYVF KIMGGCDKQG FPMKQGVLTP GRVRLLLYRG TPCFRGYGR RNGERRRKSV RGCIVSPDLS VLNLVIVKKG ENDLPGLTDT EKPRMRGPKR ASKIRKLFNL SKEDDVRKYV N TYRRNFTT ...String:
MKFNIANPTT GCQKKLEIDD DQKLRAFFDK RISQEVSGDS LGEEFKGYVF KIMGGCDKQG FPMKQGVLTP GRVRLLLYRG TPCFRGYGR RNGERRRKSV RGCIVSPDLS VLNLVIVKKG ENDLPGLTDT EKPRMRGPKR ASKIRKLFNL SKEDDVRKYV N TYRRNFTT KTGKNASKAP KIQRLVTPLT LQRKRARIAD KKKRIAKAKS EAADYQKLLA SRLKEQRERR SESLAKKRSR LS AASKPSI AA

UniProtKB: 40S ribosomal protein S6

+
Macromolecule #15: 40S body ribosomal protein uS4

MacromoleculeName: 40S body ribosomal protein uS4 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 23.051686 KDa
SequenceString: MVHVSFYRNY GKTFKKPRRP YEKERLDAEL KLVGEYGLRC KRELWRVQYA LSRIRNAARM LLTLDEKDPR RIFEGEALLR RMNRYGLLD ESQNKLDYVL ALTVENFLER RLQTLVFKTG MAKSIHHARV LIRQRHIRVG RQVVNVASFM VRVDSQKHID F SLTSPFGG ...String:
MVHVSFYRNY GKTFKKPRRP YEKERLDAEL KLVGEYGLRC KRELWRVQYA LSRIRNAARM LLTLDEKDPR RIFEGEALLR RMNRYGLLD ESQNKLDYVL ALTVENFLER RLQTLVFKTG MAKSIHHARV LIRQRHIRVG RQVVNVASFM VRVDSQKHID F SLTSPFGG GRPGRVKRKN QKSAAKKAAG GDGDEEDEE

UniProtKB: Uncharacterized protein

+
Macromolecule #16: 30S ribosomal protein S15, chloroplastic

MacromoleculeName: 30S ribosomal protein S15, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 17.099254 KDa
SequenceString:
MGRMHSRGKG ISASALPYKR TPPSWLKISA PDVEDNICKF AKKGLTPSQI GVILRDSHGI AQVKSVTGSK ILRILKAHGL APEIPEDLY HLIKKAVAIR KHLERNRKDK DSKFRLILVE SRIHRLARYY KKTKKLPPVW KYESTTASTL VA

UniProtKB: Small ribosomal subunit protein uS15 N-terminal domain-containing protein

+
Macromolecule #17: Ribosomal protein S14

MacromoleculeName: Ribosomal protein S14 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 16.389855 KDa
SequenceString:
MSKRRTREPK EETVTLGPSV REGELVFGVA HIFASFNDTF IHVTDLSGRE TMVRITGGMK VKADRDESSP YAAMLAAQDV SQRCKELGI NALHIKLRAT GGNKTKTPGP GAQSALRALA RSGMKIGRIE DVTPIPT(IAS)ST RRKGGRRGRR L

UniProtKB: Ribosomal protein S14

+
Macromolecule #18: 40S ribosomal protein S24

MacromoleculeName: 40S ribosomal protein S24 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 15.445315 KDa
SequenceString:
MADKAVTIRT RKFMTNRLLA RKQFIIDVLH PGRANVSKAE LKEKLSRMYE VKDPNAIFVF KFRTHFGGGK STGFGLIYDS VENAKKYEP KYRLIRNGLD TKVEKSRKQM KERKNRAKKV RGVKKTKAGD AKKK

UniProtKB: 40S ribosomal protein S24

+
Macromolecule #19: 40S ribosomal protein S27

MacromoleculeName: 40S ribosomal protein S27 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 9.620199 KDa
SequenceString:
MVLPNDVDLL NPPAEHEKKK HKLKRLVQSP NSFFMDVKCQ GCFNITTVFS HSQTVVVCGN CQTVLCQPTG GRARLIEGCS FRRKGD

UniProtKB: 40S ribosomal protein S27

+
Macromolecule #20: 40S ribosomal protein S30

MacromoleculeName: 40S ribosomal protein S30 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 6.953253 KDa
SequenceString:
MGKVHGSLAR AGKVRGQTPK VAKQDKKKKP RGRAHKRMQY NRRFVTAVVG FGKKRGPNSS EK

UniProtKB: 40S ribosomal protein S30

+
Macromolecule #21: 40S ribosomal protein S15a-1

MacromoleculeName: 40S ribosomal protein S15a-1 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 14.551979 KDa
SequenceString:
MVRVSVLNDA LKSMYNAEKA GKAQVELRPS SKVIIKFLIV MQKHGYIGDF QYVDDHRVGK IVVELNGRLN KCGVISPRFD VGVATIEGW TARLLPSRQF GYIVLTTSAG IMDHEEARRK NVGGKVLGFF Y

UniProtKB: 40S ribosomal protein S15a-1

+
Macromolecule #22: Ribosomal protein L19

MacromoleculeName: Ribosomal protein L19 / type: protein_or_peptide / ID: 22 / 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

+
Macromolecule #23: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 23 / Number of copies: 19 / Formula: K
Molecular weightTheoretical: 39.098 Da

+
Macromolecule #24: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 24 / Number of copies: 60 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #25: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 25 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #26: water

MacromoleculeName: water / type: ligand / ID: 26 / Number of copies: 570 / 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

-
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: 2.53 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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