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- PDB-7qiy: Specific features and methylation sites of a plant ribosome. 40S ... -

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Entry
Database: PDB / ID: 7qiy
TitleSpecific features and methylation sites of a plant ribosome. 40S head ribosomal subunit.
Components
  • (40S head ribosomal protein ...) x 5
  • (40S ribosomal protein ...) x 3
  • 18S rRNA head
  • KH type-2 domain-containing protein
  • Mitogen-activated protein kinase
  • Ribosomal_S10 domain-containing protein
  • Ribosomal_S7 domain-containing protein
  • S10_plectin domain-containing protein
  • mRNA
  • tRNA
KeywordsRIBOSOME / Solanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA
Function / homology
Function and homology information


MAP kinase activity / JUN 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 / cytoplasmic translation ...MAP kinase activity / JUN 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 / cytoplasmic translation / intracellular signal transduction / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SPARK domain / SPARK / Ribosomal Protein S7 / Ribosomal protein S7/S5 / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. ...SPARK domain / SPARK / Ribosomal Protein S7 / Ribosomal protein S7/S5 / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / 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 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / 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 S13-like, H2TH / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / 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 / Ribosomal protein S5 domain 2-type fold / WD40 repeat, conserved site / 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 / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
beta-D-glucopyranose / : / 1,4-DIAMINOBUTANE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S29 / Small ribosomal subunit protein uS10 domain-containing protein ...beta-D-glucopyranose / : / 1,4-DIAMINOBUTANE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / 30S ribosomal protein S3, chloroplastic / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsCottilli, P. / Itoh, Y. / Amunts, A.
Funding supportEuropean Union, 4items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107European Union
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080European Union
European Molecular Biology Organization (EMBO)H2020-MSCA-IF-2017European Union
CitationJournal: Plant Commun / Year: 2022
Title: Cryo-EM structure and rRNA modification sites of a plant ribosome.
Authors: Patrick Cottilli / Yuzuru Itoh / Yuko Nobe / Anton S Petrov / Purificación Lisón / Masato Taoka / Alexey Amunts /
Abstract: Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to ...Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.
History
DepositionDec 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: 18S rRNA head
D: KH type-2 domain-containing protein
E: Ribosomal_S7 domain-containing protein
F: S10_plectin domain-containing protein
G: 40S head ribosomal protein uS19
H: 40S head ribosomal protein uS9
I: 40S ribosomal protein S17
J: 40S head ribosomal protein uS13
K: 40S head ribosomal protein eS19
L: Ribosomal_S10 domain-containing protein
M: 40S head ribosomal protein eS28
N: 40S ribosomal protein S29
O: Mitogen-activated protein kinase
P: 40S ribosomal protein S25
Q: tRNA
R: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)819,88357
Polymers818,47716
Non-polymers1,40541
Water4,053225
1


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

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Components

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RNA chain , 3 types, 3 molecules 2QR

#1: RNA chain 18S rRNA head


Mass: 582941.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: GenBank: 2090998067
#15: RNA chain tRNA


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


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

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Protein , 5 types, 5 molecules DEFLO

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


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


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


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


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


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

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40S head ribosomal protein ... , 5 types, 5 molecules GHJKM

#5: Protein 40S head ribosomal protein uS19


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


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


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


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


Mass: 7551.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4B4Z0

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40S ribosomal protein ... , 3 types, 3 molecules INP

#7: Protein 40S ribosomal protein S17


Mass: 16251.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: P49215
#12: Protein 40S ribosomal protein S29


Mass: 6455.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A1U7V0A7
#14: Protein 40S ribosomal protein S25


Mass: 11995.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7F3F2

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Sugars , 1 types, 1 molecules

#20: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


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

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Non-polymers , 5 types, 265 molecules

#17: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#18: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2
#19: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Mg
#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 40S head ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Solanum lycopersicum (tomato)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4GctfCTF correction
10RELION3initial Euler assignment
11RELION3.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335806 / Symmetry type: POINT

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