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- PDB-9sdq: Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subun... -

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Basic information

Entry
Database: PDB / ID: 9sdq
TitleCryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head)
Components
  • (Small ribosomal subunit protein ...) x 12
  • RNA (500-MER)
KeywordsRIBOSOME / Ribosomal 40S subunit -Head region
Function / homology
Function and homology information


plant-type cell wall / plasmodesma / plant-type vacuole / vacuole / plastid / cytosolic ribosome / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation ...plant-type cell wall / plasmodesma / plant-type vacuole / vacuole / plastid / cytosolic ribosome / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / peroxisome / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / defense response to bacterium / rRNA binding / structural constituent of ribosome / ribosome / translation / mRNA binding / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 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. ...Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 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 S19A/S15e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 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. / : / 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. / K homology domain-like, alpha/beta / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S13-like, H2TH / 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 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 / Winged helix DNA-binding domain superfamily / Ribosomal protein S5 domain 2-type fold / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS13z/uS13y/uS13x / Small ribosomal subunit protein eS28x / Small ribosomal subunit protein uS10z/uS10x / Small ribosomal subunit protein uS14z/uS14y/uS14x / Small ribosomal subunit protein eS19x / Small ribosomal subunit protein uS19x ...: / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS13z/uS13y/uS13x / Small ribosomal subunit protein eS28x / Small ribosomal subunit protein uS10z/uS10x / Small ribosomal subunit protein uS14z/uS14y/uS14x / Small ribosomal subunit protein eS19x / Small ribosomal subunit protein uS19x / Small ribosomal subunit protein eS10x / Small ribosomal subunit protein eS17w / Small ribosomal subunit protein eS25y / Small ribosomal subunit protein uS3z / Small ribosomal subunit protein uS9z / Small ribosomal subunit protein uS7z
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSudeep, K. / Lu, X. / Paatero, A.O. / Ruonala, R. / Tranter, D. / Guryanov, S. / Rehan, S. / Hellmann, E. / Haakonsson, A. / Butcher, S.J. ...Sudeep, K. / Lu, X. / Paatero, A.O. / Ruonala, R. / Tranter, D. / Guryanov, S. / Rehan, S. / Hellmann, E. / Haakonsson, A. / Butcher, S.J. / Huiskonen, J.T. / Kajander, T. / Helariutta, Y. / Paavilainen, V.O.
Funding support United States, Finland, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132649[PVO1] United States
Academy of Finland338836 Finland
Academy of Finland314672 Finland
CitationJournal: To Be Published
Title: Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head)
Authors: Sudeep, K. / Paavilainen, V.O.
History
DepositionAug 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: RNA (500-MER)
BD: Small ribosomal subunit protein uS3z
BF: Small ribosomal subunit protein uS7z
BP: Small ribosomal subunit protein uS19x
BQ: Small ribosomal subunit protein uS9z
BS: Small ribosomal subunit protein uS13z/uS13y/uS13x
BT: Small ribosomal subunit protein eS19x
BU: Small ribosomal subunit protein uS10z/uS10x
Bc: Small ribosomal subunit protein eS28x
d: Small ribosomal subunit protein uS14z/uS14y/uS14x
e: Small ribosomal subunit protein eS25y
BK: Small ribosomal subunit protein eS10x
BR: Small ribosomal subunit protein eS17w
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,71418
Polymers353,50713
Non-polymers2075
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain RNA (500-MER)


Mass: 160514.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

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Small ribosomal subunit protein ... , 12 types, 12 molecules BDBFBPBQBSBTBUBcdeBKBR

#2: Protein Small ribosomal subunit protein uS3z / 40S ribosomal protein S3-1


Mass: 27559.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SIP7
#3: Protein Small ribosomal subunit protein uS7z / 40S ribosomal protein S5-1 / AtRPS5B


Mass: 23025.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZUT9
#4: Protein Small ribosomal subunit protein uS19x / 40S ribosomal protein S15-4


Mass: 17106.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FY64
#5: Protein Small ribosomal subunit protein uS9z / 40S ribosomal protein S16-1


Mass: 16663.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SK22
#6: Protein Small ribosomal subunit protein uS13z/uS13y/uS13x / 40S ribosomal protein S18


Mass: 17582.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P34788
#7: Protein Small ribosomal subunit protein eS19x / 40S ribosomal protein S19-3


Mass: 15627.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FNP8
#8: Protein Small ribosomal subunit protein uS10z/uS10x / 40S ribosomal protein S20-1


Mass: 13903.319 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49200
#9: Protein Small ribosomal subunit protein eS28x / 40S ribosomal protein S28-2


Mass: 7355.558 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P34789
#10: Protein Small ribosomal subunit protein uS14z/uS14y/uS14x / 40S ribosomal protein S29


Mass: 6443.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q680P8
#11: Protein Small ribosomal subunit protein eS25y / 40S ribosomal protein S25-2


Mass: 12095.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SIK2
#12: Protein Small ribosomal subunit protein eS10x / 40S ribosomal protein S10-3


Mass: 19581.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LTF2
#13: Protein Small ribosomal subunit protein eS17w / 40S ribosomal protein S17-4


Mass: 16048.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LZ17

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Non-polymers , 3 types, 5 molecules

#14: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 40S SSU Arabidopsis (root) ribosome complex / Type: RIBOSOME / Entity ID: #1-#13 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
Details: 50 mM Hepes, pH 7.4, 5 mM MgAc, 100 mM KAc, pH 7.5, 1 mM DTT, Complete protease inhibitor
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 10500 X / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 24.512 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115070 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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