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- PDB-8r57: CryoEM structure of wheat 40S ribosomal subunit, head domain -

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Basic information

Entry
Database: PDB / ID: 8r57
TitleCryoEM structure of wheat 40S ribosomal subunit, head domain
Components
  • (40S ribosomal protein ...) x 8
  • (Ribosomal protein ...) x 2
  • (Small ribosomal subunit protein ...) x 2
  • Plectin/eS10 N-terminal domain-containing protein
  • Putative ribosomal protein S18
  • RNA (458-MER)
  • Ubiquitin-like domain-containing protein
KeywordsRIBOSOME / small ribosomal subunit / wheat / eukaryotes / 40S
Function / homology
Function and homology information


plastid / translation regulator activity / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / protein kinase C binding / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit ...plastid / translation regulator activity / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / protein kinase C binding / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
: / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a ...: / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S19e signature. / Ribosomal S17 / Ribosomal protein S19e / 40S Ribosomal protein S10 / Ribosomal protein S28e conserved site / Ribosomal protein S28e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S28e / Ribosomal protein S28e signature. / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ribosomal protein S3, conserved site / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ubiquitin family / Ribosomal protein S14 / Type-2 KH domain profile. / Ribosomal protein S13/S18 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ubiquitin homologues / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / Ribosomal protein S9, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S13 family profile. / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ubiquitin-like domain / Ribosomal protein S7p/S5e / Ribosomal protein S9/S16 / Ribosomal protein S9 signature. / Ubiquitin domain profile. / Zinc-binding ribosomal protein / Ribosomal protein S5 domain 2-type fold, subgroup / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Ribosomal protein S5 domain 2-type fold / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S17 / 40S ribosomal protein S15 / Small ribosomal subunit protein uS14 / Putative ribosomal protein S18 / Ribosomal protein S20 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S17 / 40S ribosomal protein S15 / Small ribosomal subunit protein uS14 / Putative ribosomal protein S18 / Ribosomal protein S20 / Ubiquitin-like domain-containing protein / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS7c / Uncharacterized protein / 40S ribosomal protein S16 / 40S ribosomal protein S28 / 40S ribosomal protein S25 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 30S ribosomal protein S3, chloroplastic
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsKravchenko, O.V. / Baymukhametov, T.N. / Afonina, Z.A. / Vasilenko, K.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit.
Authors: Olesya V Kravchenko / Timur N Baymukhametov / Zhanna A Afonina / Konstantin S Vassilenko /
Abstract: Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has ...Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has been resolved to date; it especially concerns plant ribosomes and ribosomal subunits. Here, we report a high-resolution cryo-electron microscopy reconstruction of the small subunit of the (common wheat) cytoplasmic ribosome. A detailed atomic model was built that includes the majority of the rRNA and some of the protein modifications. The analysis of the obtained data revealed structural peculiarities of the 40S subunit in the monocot plant ribosome. We applied the 3D Flexible Refinement approach to analyze the internal mobility of the 40S subunit and succeeded in decomposing it into four major motions, describing rotations of the head domain and a shift in the massive rRNA expansion segment. It was shown that these motions are almost uncorrelated and that the 40S subunit is flexible enough to spontaneously adopt any conformation it takes as a part of a translating ribosome or ribosomal complex. Here, we introduce the first high-resolution structure of an isolated plant 40S subunit and the first quantitative analysis of the flexibility of small ribosomal subunits, hoping that it will help in studying various aspects of ribosome functioning.
History
DepositionNov 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Plectin/eS10 N-terminal domain-containing protein
M: 40S ribosomal protein S12
F: 40S ribosomal protein S3
P: Small ribosomal subunit protein uS7c
Q: 40S ribosomal protein S16
U: Ribosomal protein S20
T: 40S ribosomal protein S19
Z: 40S ribosomal protein S25
c: 40S ribosomal protein S28
d: Small ribosomal subunit protein uS14
g: Ribosomal protein RACK1 subfamily. WD repeat G protein beta family
S: Putative ribosomal protein S18
R: 40S ribosomal protein S15
h: 40S ribosomal protein S17
A: RNA (458-MER)
f: Ubiquitin-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)848,23044
Polymers847,37916
Non-polymers85228
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules KSf

#1: Protein Plectin/eS10 N-terminal domain-containing protein


Mass: 20463.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5AUH7
#12: Protein Putative ribosomal protein S18 /


Mass: 17702.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L806
#16: Protein Ubiquitin-like domain-containing protein


Mass: 17692.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5A9E1

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40S ribosomal protein ... , 8 types, 8 molecules MFQTZcRh

#2: Protein 40S ribosomal protein S12 /


Mass: 15364.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FEZ3
#3: Protein 40S ribosomal protein S3 /


Mass: 25398.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5I1R7
#5: Protein 40S ribosomal protein S16 /


Mass: 16856.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5DS33
#7: Protein 40S ribosomal protein S19 /


Mass: 17097.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FWF5
#8: Protein 40S ribosomal protein S25 /


Mass: 12094.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5EP45
#9: Protein 40S ribosomal protein S28 /


Mass: 7477.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5E8X2
#13: Protein 40S ribosomal protein S15 /


Mass: 17295.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6LV48
#14: Protein 40S ribosomal protein S17 /


Mass: 16479.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5XY60

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Small ribosomal subunit protein ... , 2 types, 2 molecules Pd

#4: Protein Small ribosomal subunit protein uS7c


Mass: 22350.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D067
#10: Protein Small ribosomal subunit protein uS14


Mass: 6392.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K3

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Ribosomal protein ... , 2 types, 2 molecules Ug

#6: Protein Ribosomal protein S20 /


Mass: 14128.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: U5HTD8
#11: Protein Ribosomal protein RACK1 subfamily. WD repeat G protein beta family / Ribosome


Mass: 36200.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D4F5

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RNA chain , 1 types, 1 molecules A

#15: RNA chain RNA (458-MER)


Mass: 584382.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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Non-polymers , 4 types, 385 molecules

#17: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#18: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#19: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#20: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Small ribosomal subunit from Triticum aestivum (common wheat)
Type: RIBOSOME / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Triticum aestivum (bread wheat) / Strain: Moskovskaya / Cellular location: cytoplasm / Organ: seed / Tissue: germ
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportFilm material: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 0.1 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 84 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6201
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 32 / Used frames/image: 0-32

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
2PHENIX1.20.1_4487:model refinement
3EPU1.9.1.16image acquisition
5Warp1.0.9CTF correction
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
13cryoSPARC4.2.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 982063
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256000 / Symmetry type: POINT

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