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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 / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / translational initiation ...plant-type cell wall / plasmodesma / plant-type vacuole / vacuole / plastid / cytosolic ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / 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 S10 / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / 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: Structure / Year: 2026
Title: Cryo-EM structure of the Arabidopsisthaliana ribosome in translating and non-translating states.
Authors: Sudeep Karki / Xun Lu / Anja O Paatero / Raili Ruonala / Dale Tranter / Sergey Guryanov / Shahid Rehan / Eva Hellmann / Anders Haakonsson / Sarah J Butcher / Juha T Huiskonen / Tommi ...Authors: Sudeep Karki / Xun Lu / Anja O Paatero / Raili Ruonala / Dale Tranter / Sergey Guryanov / Shahid Rehan / Eva Hellmann / Anders Haakonsson / Sarah J Butcher / Juha T Huiskonen / Tommi Kajander / Yrjö Helariutta / Ville O Paavilainen /
Abstract: Translational control of mRNA expression underpins much of post-transcriptional gene expression driving developmental processes in eukaryotes. How ribosomal mRNA translation is executed in plants may ...Translational control of mRNA expression underpins much of post-transcriptional gene expression driving developmental processes in eukaryotes. How ribosomal mRNA translation is executed in plants may be especially important for adapting to an ever-changing environment. Arabidopsis thaliana is the main genetic model organism in plant science, yet structural insights into developmental processes where ribosomal gene expression plays important roles currently remain lacking. Here, we present cryoelectron microscopy (cryo-EM) structures of the Arabidopsis cytosolic ribosome in both translating and non-translating states, which together provide new structural details into how translation of cytosolic mRNAs is coordinated. Our structures reveal detailed information on the interactions of tRNAs, mRNA, and the nascent polypeptide with subunits of the actively translating 80S ribosome and the role of ribosomal RNA methylation in stabilizing ribosomal subunits. The structures provide a foundation for interpreting the functional effects of many mutations of ribosomal proteins affecting phenotypic effects for plant tissue development.
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
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Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jul 8, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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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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