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- EMDB-14003: Specific features and methylation sites of a plant ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-14003
TitleSpecific features and methylation sites of a plant ribosome
Map data
Sample
  • Complex: 40S head ribosomal subunit
    • RNA: x 3 types
    • Protein or peptide: x 13 types
  • Ligand: x 6 types
KeywordsSolanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA / RIBOSOME
Function / homology
Function and homology information


MAP kinase activity / translation regulator activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / rRNA binding / intracellular signal transduction ...MAP kinase activity / translation regulator activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / rRNA binding / intracellular signal transduction / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SPARK domain / SPARK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal ...SPARK domain / SPARK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S14/S29 / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S13-like, H2TH / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S5 domain 2-type fold, subgroup / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Ribosomal protein S5 domain 2-type fold / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Protein kinase domain / WD40/YVTN repeat-like-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / Nucleic acid-binding, OB-fold / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
40S ribosomal protein S29 / Small ribosomal subunit protein uS10 domain-containing protein / 40S ribosomal protein S25 / 40S ribosomal protein S15 / 40S ribosomal protein S18 / 40S ribosomal protein S19 / 40S ribosomal protein S16 / Protein kinase domain-containing protein / KH type-2 domain-containing protein / Small ribosomal subunit protein uS7 domain-containing protein ...40S ribosomal protein S29 / Small ribosomal subunit protein uS10 domain-containing protein / 40S ribosomal protein S25 / 40S ribosomal protein S15 / 40S ribosomal protein S18 / 40S ribosomal protein S19 / 40S ribosomal protein S16 / Protein kinase domain-containing protein / KH type-2 domain-containing protein / Small ribosomal subunit protein uS7 domain-containing protein / Plectin/eS10 N-terminal domain-containing protein / 40S ribosomal protein S28 / Small ribosomal subunit protein eS17
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsAmunts A / Cottilli P
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_14003.png

Downloads & links

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Map

FileDownload / File: emd_14003.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: 0.0197
Minimum - Maximum-0.15170632 - 0.3395055
Average (Standard dev.)-0.0009627114 (±0.0035361608)
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_14003_msk_1.map
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Half map: #1

Fileemd_14003_half_map_1.map
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Half map: #2

Fileemd_14003_half_map_2.map
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Sample components

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Entire : 40S head ribosomal subunit

EntireName: 40S head ribosomal subunit
Components
  • Complex: 40S head ribosomal subunit
    • RNA: 18S rRNA head
    • Protein or peptide: KH type-2 domain-containing protein
    • Protein or peptide: Ribosomal_S7 domain-containing protein
    • Protein or peptide: S10_plectin domain-containing protein
    • Protein or peptide: 40S head ribosomal protein uS19
    • Protein or peptide: 40S head ribosomal protein uS9
    • Protein or peptide: 40S ribosomal protein S17
    • Protein or peptide: 40S head ribosomal protein uS13
    • Protein or peptide: 40S head ribosomal protein eS19
    • Protein or peptide: Ribosomal_S10 domain-containing protein
    • Protein or peptide: 40S head ribosomal protein eS28
    • Protein or peptide: 40S ribosomal protein S29
    • Protein or peptide: Mitogen-activated protein kinase
    • Protein or peptide: 40S ribosomal protein S25
    • RNA: tRNA
    • RNA: mRNA
  • Ligand: POTASSIUM ION
  • Ligand: 1,4-DIAMINOBUTANE
  • Ligand: MAGNESIUM ION
  • Ligand: beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: 40S head ribosomal subunit

SupramoleculeName: 40S head ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Solanum lycopersicum (tomato)

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Macromolecule #1: 18S rRNA head

MacromoleculeName: 18S rRNA head / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 582.941625 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 A(PSU)UUAA GUU G(OMU)UGCAGUU(A2M) AAAAGCUCGU AG(PSU)UGGACUU UGGGAUGGGC CGGCCGGUCC GCCCUAGGUG UGCAC CGGU CGUCUCGUCC CUUCUGUCGG CGAUGCGCUC CUGGCCUUAA UUGGCCGGGU CGUGCCUCCG GCGCUGUUAC U(PSU) UGAAGAA A(PSU)UAGAGUGC UCAAAGCAAG CCUACGCUCU GUAUACAUU(A2M) GCAUGGGA(PSU)A ACAUUAUAGG A UUUCGGUC CUAUUACGUU GGCCUUCGGG AUCGGAGUAA UGAUUAACAG GGACAGUCGG GGGCAUUCGU AUUUCAUAGU CA GAGGUGA AAU(PSU)CUUGGA UUUAUGAAAG ACGAACAACU GCGAAAGCAU (PSU)(PSU)GCCAAGGA UGUUUUCAUU A AUCAAGA(A2M) CGAAAGUUGG GGGCUCGAAG ACGA(PSU)CAGAU ACCG(OMU)CCUAG UCUCAACCA(PSU) AAACGA UGC CGACCAGGGA UCGGCGGAUG UUGCUUUUAG GACUCCGCCG GCACCUUAUG AGAAAUCAAA GUUUUUGGG(PSU) UCC GGGGGG AGUA(PSU)GGUCG CAAGGCUGAA ACUUAAAGGA AUUGACGGAA GGGCACCACC AGGAGUGGAG CC(PSU)GCG GC(PSU) UAAUU(PSU)GAC(I2T) CAACACGGGG AAACU(PSU)ACCA GG(PSU)(OMC)CAGACA UAGUAAGGAU UGA CAGACU GAGAGCUCUU UCUUGAUUC(OMU) A(OMU)GGGUGG(OMU)G (OMG)UGCAUGGC(4AC) GUUCUUAGU(PSU) GGUGGAGCG A(PSU)UUG(PSU)CUGG (PSU)UAAUUCCGU UAACGA(A2M)CGA GACCUCAGCC UGCUAACUAG CUAUG CGGA GGUAUCCCUU CGCGGCCAGC U(OMU)CUUAGAGG GACUACGGCC UUUUAGGCCG CGGAAGUUUG AGGCAAUAAC A (OMG)GUCUGUG AUGCCC(OMU)UAG AUGUUCUGGG CCGCACGCGC GCUACACUGA UGUA(PSU)UCAAC GAGCUUAUAG CCUUGGCCG ACAGGCCCGG GUAAUCUUUG AAAUU(PSU)CA(PSU)C GUGAUGGGGA UAGAUCAUUG CAAUUGU(PSU)G GUCUUCAACG (A2M)G(7MG)AAUUCCU AGUAAGCGCG AGUCAUCAGC UCGCGUUGAC UACGUCCCUG CCCUU(PSU)GU A CACACCG(OMC)CC GUCGCUCCUA CCGAUUGAAU GAUCCGGUGA AAUGUUCGGA UCGCGGCGAC GUGGGCGGUU CGCUG CCCG CGACGUCGCG AGAAGUCCAU UGAACCUUAU CAUUUAGAGG A(A2M)GGAGAAGU CGUA(6MZ)CAAGG UUUCGUAG G UG(MA6)(MA6)CCUGCG GAAGGAUCAU UG

GENBANK: GENBANK: OK073663.1

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Macromolecule #15: tRNA

MacromoleculeName: tRNA / type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 4.470731 KDa
SequenceString:
AGGCUGAUAA CCUA

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Macromolecule #16: mRNA

MacromoleculeName: mRNA / type: rna / ID: 16 / Number of copies: 1
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 895.596 Da
SequenceString:
AUC

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Macromolecule #2: KH type-2 domain-containing protein

MacromoleculeName: KH type-2 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 26.828357 KDa
SequenceString: MAKQSVQMSK KRKFVADGVF FAELNEVLTR ELAEDGYSGV EVRVTPMRTE IIIRATRTQN VLGDKGRRIR ELTSVVQKRF NFDENTVEL YAEKVNNRGL CAIAQAESLR YKLLGGLAVR RACYGVLRFI MESGAKGCEV IVSGKLRAQR AKSMKFKDGY M ISSGQPVK ...String:
MAKQSVQMSK KRKFVADGVF FAELNEVLTR ELAEDGYSGV EVRVTPMRTE IIIRATRTQN VLGDKGRRIR ELTSVVQKRF NFDENTVEL YAEKVNNRGL CAIAQAESLR YKLLGGLAVR RACYGVLRFI MESGAKGCEV IVSGKLRAQR AKSMKFKDGY M ISSGQPVK EYIDSAVRHV LLRQGVLGIK VKIMLDWDPK GKQGPTTPLP DLVTIHPPKE EEEYLRLPVA APVEIDPPIV V

UniProtKB: KH type-2 domain-containing protein

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Macromolecule #3: Ribosomal_S7 domain-containing protein

MacromoleculeName: Ribosomal_S7 domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 23.686199 KDa
SequenceString: MEEASVVAVD NQKPQQEKPH TDVLLFNRWS YDGVQIADMS VEDYITATAN KHPTYMPHTA GRYQAKRFRK AQCPIVERLT NSLMMHGRN NGKKLMAVRI IKHAMEIIHL LTDQNPIQVI VDAVINSGPR EDATRIGSAG VVRRQAVDIS PLRRVNQAIY L LTTGARES ...String:
MEEASVVAVD NQKPQQEKPH TDVLLFNRWS YDGVQIADMS VEDYITATAN KHPTYMPHTA GRYQAKRFRK AQCPIVERLT NSLMMHGRN NGKKLMAVRI IKHAMEIIHL LTDQNPIQVI VDAVINSGPR EDATRIGSAG VVRRQAVDIS PLRRVNQAIY L LTTGARES AFRNIKTIAE CLADELINAA KGSSNSYAIK KKDEIERVAK ANR

UniProtKB: Small ribosomal subunit protein uS7 domain-containing protein

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Macromolecule #4: S10_plectin domain-containing protein

MacromoleculeName: S10_plectin domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 19.882539 KDa
SequenceString:
MIIPEKNRRE ISKYLFQEGV CFAKKDYNLA KHPNIDVPNL QVIKLMQSFK SKEYVRETFA WMHYYWYLTN DGIEFLRTYL NLPSEIVPA TLKKSAKPLG RPMGGPPGDR PRGPPRFEGD RPRFGDRDGY RAGPRGPPGE FGGEKGGAPA DYQPAFRGGG G RPGFGRGA GGFGGAPPSS SS

UniProtKB: Plectin/eS10 N-terminal domain-containing protein

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Macromolecule #5: 40S head ribosomal protein uS19

MacromoleculeName: 40S head ribosomal protein uS19 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 17.352471 KDa
SequenceString:
MAEVEADVAT GQPRKRTFKK FSYRGVDLDS LLDMSTDELV KLYPARPRRR FQRGLKRKPM ALIKKLRKAK REAPQGEKPE VVRTHLRNM IIVPEMIGSV IGIYNGKTFN QIEVKPEMIS HYLAEFSISY KPVKHGRPGI GATHSSRFIP LK

UniProtKB: 40S ribosomal protein S15

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Macromolecule #6: 40S head ribosomal protein uS9

MacromoleculeName: 40S head ribosomal protein uS9 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 16.805812 KDa
SequenceString:
MQAAPATVES VQCFGRKKTA VAVTHCKRGR GLIKINGVPI ELVQPEILRY KAFEPILLLG RHRFAGVDMR IRVKGGGHTS QIYAIRQSI AKALVAFYQK YVDEQQKKEI KDILIRYDRT LLVADPRRCE PKKFGGRGAR SRFQKSYR

UniProtKB: 40S ribosomal protein S16

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Macromolecule #7: 40S ribosomal protein S17

MacromoleculeName: 40S ribosomal protein S17 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 16.251941 KDa
SequenceString:
MGRVRTKTVK KSSRQVIERY YSKMTLDFHT NKKILEEVAI IPSKRLRNKI AGFSTHLMKR IQKGPVRGIS LKLQEEERER RMDFVPDES AIKTDLIEVD KETLDMLSAL GMSDLPGVVK QAAEPQAVAA LPSYGRGGGG FGRKY

UniProtKB: Small ribosomal subunit protein eS17

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Macromolecule #8: 40S head ribosomal protein uS13

MacromoleculeName: 40S head ribosomal protein uS13 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 17.574461 KDa
SequenceString:
MSLVANEEFQ HILRVQNTNV DGKQKIMFAL TSIKGIGRRF ANIACKKADI DMNKRAGELT AAELDSLMVV VANPRQFKIP DWFLNRQKD YKDGKFSQVT SNALDMKLRD DLERLKKIRN HRGLRHYWGL RVRGQHTKTT GRRGKTVGVS KKR

UniProtKB: 40S ribosomal protein S18

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Macromolecule #9: 40S head ribosomal protein eS19

MacromoleculeName: 40S head ribosomal protein eS19 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 16.056355 KDa
SequenceString:
MEPARSVKDV SPHDFVKAYA AHLKRSGKLE LPEWTDIVKT GKLKELAPYD PDWYYIRAAS MARKIYLRGG IGVGGFRRIY GGNQRNGSR PRHFCKSSGS VARHILQQLQ TMNIIDFDPK GGRRITSNGQ RDLDQVAGRI SAAN

UniProtKB: 40S ribosomal protein S19

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Macromolecule #10: Ribosomal_S10 domain-containing protein

MacromoleculeName: Ribosomal_S10 domain-containing protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 13.735125 KDa
SequenceString:
MAAYAAMKPT KPGLEEPAEM IHKIRITLSS KNVKNLEKVC ADLVRGAKDK RLRVKGPVRM PTKVLNITTR KSPCGEGTNT WDRFELRVH KRVIDLFSSP DVVKQITSIT IEPGVEVEVT IAES

UniProtKB: Small ribosomal subunit protein uS10 domain-containing protein

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Macromolecule #11: 40S head ribosomal protein eS28

MacromoleculeName: 40S head ribosomal protein eS28 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 7.551849 KDa
SequenceString:
MESVTKHAIV IKIMGRTGSR GQVTQVRVKF LDDQNRFIMR NVKGPVREGD ILTLLESERE ARRLR

UniProtKB: 40S ribosomal protein S28

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Macromolecule #12: 40S ribosomal protein S29

MacromoleculeName: 40S ribosomal protein S29 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 6.455581 KDa
SequenceString:
MGHSNIWNAH PKNYGPGSRT CRVCGNPHAI IRKYGLMCCR QCFRSNAKEI GFIKYR

UniProtKB: 40S ribosomal protein S29

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Macromolecule #13: Mitogen-activated protein kinase

MacromoleculeName: Mitogen-activated protein kinase / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 35.993617 KDa
SequenceString: MSQESLVLRG TMKAHTDWVT AIATPIDNSD MIVTSSRDKS IIVWSLTKDG SQYGVPRRRL TGHGHFVEDV VLSSDGMFAL SGSWDGELR LWDLQAGTTA RRFVGHTKDV LSVAFSVDNR QIVSASRDKT IKLWNTLGEC KYTIQEQDSH SDWVSCVRFS P NNLQPTIV ...String:
MSQESLVLRG TMKAHTDWVT AIATPIDNSD MIVTSSRDKS IIVWSLTKDG SQYGVPRRRL TGHGHFVEDV VLSSDGMFAL SGSWDGELR LWDLQAGTTA RRFVGHTKDV LSVAFSVDNR QIVSASRDKT IKLWNTLGEC KYTIQEQDSH SDWVSCVRFS P NNLQPTIV SGSWDRTVKI WNLTNCKLRS TLAGHSGYVN TVAVSPDGSL CASGGKDGVI LLWDLAEGKK LYSLDAGSII HT LCFSPNR YWLCAATESS IKIWDLESKS IVVDLKVDLK QESEMFGTAA TDSKTKVIYC TSLSWSADGS TLFSGYTDGL IRV WGIGRY

UniProtKB: Protein kinase domain-containing protein

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Macromolecule #14: 40S ribosomal protein S25

MacromoleculeName: 40S ribosomal protein S25 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 11.995226 KDa
SequenceString:
MAPKKEKAPP PSSKPAKSGG GKQKKKKWSK GKQKEKVNNM VLFDKGTYDK LITEAPKYKL ITPSVLSDRL RISGSLARKA IRELMAKGL IRMVSAHASQ QIYTRATNT

UniProtKB: 40S ribosomal protein S25

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Macromolecule #17: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 17 / Number of copies: 10 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #18: 1,4-DIAMINOBUTANE

MacromoleculeName: 1,4-DIAMINOBUTANE / type: ligand / ID: 18 / Number of copies: 1 / Formula: PUT
Molecular weightTheoretical: 88.151 Da
Chemical component information

ChemComp-PUT:
1,4-DIAMINOBUTANE

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Macromolecule #19: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 19 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #20: beta-D-glucopyranose

MacromoleculeName: beta-D-glucopyranose / type: ligand / ID: 20 / Number of copies: 1 / Formula: BGC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BGC:
beta-D-glucopyranose

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Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #22: water

MacromoleculeName: water / type: ligand / ID: 22 / Number of copies: 225 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3883

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.58 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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