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- PDB-9sdp: Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit -

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Basic information

Entry
Database: PDB / ID: 9sdp
TitleCryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit
Components
  • (Small ribosomal subunit protein ...) x 19
  • 18S RNA
KeywordsRIBOSOME / Arabidopsis / CryoEM
Function / homology
Function and homology information


trichome morphogenesis / cytokinesis by cell plate formation / leaf morphogenesis / chloroplast organization / plant-type cell wall / plasmodesma / plant-type vacuole / plastid / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...trichome morphogenesis / cytokinesis by cell plate formation / leaf morphogenesis / chloroplast organization / plant-type cell wall / plasmodesma / plant-type vacuole / plastid / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / chloroplast / rRNA processing / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / defense response to bacterium / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal ...: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S7e signature. / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S27e signature. / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S8e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / : / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / Ribosomal S11, conserved site
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS17z / Small ribosomal subunit protein uS11x / Small ribosomal subunit protein uS8z/uS8w / Small ribosomal subunit protein uS12y ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS17z / Small ribosomal subunit protein uS11x / Small ribosomal subunit protein uS8z/uS8w / Small ribosomal subunit protein uS12y / Small ribosomal subunit protein eS30z/eS30y/eS30x / Small ribosomal subunit protein eS6y / Small ribosomal subunit protein uS15y / Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v / Small ribosomal subunit protein uS2y / Small ribosomal subunit protein eS8z / Small ribosomal subunit protein eS4z / Small ribosomal subunit protein eS7z / Small ribosomal subunit protein eS1z / Small ribosomal subunit protein uS4y / Small ribosomal subunit protein eS26x / Small ribosomal subunit protein eS27y / Small ribosomal subunit protein eS21z / Small ribosomal subunit protein uS5w / Small ribosomal subunit protein eS24z
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKarki, S. / Lu, X. / Paatero, A.O. / Ruonala, R. / Tranter, D. / Guryanov, S. / Rehan, S. / Hellmann, E. / Haakonsson, A. / Butcher, S.J. ...Karki, S. / 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, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132649[PVO1] United States
Academy of Finland338836 and 314672 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
9: 18S RNA
BA: Small ribosomal subunit protein uS2y
BB: Small ribosomal subunit protein eS1z
BC: Small ribosomal subunit protein uS5w
BE: Small ribosomal subunit protein eS4z
BG: Small ribosomal subunit protein eS6y
BH: Small ribosomal subunit protein eS7z
BI: Small ribosomal subunit protein eS8z
BJ: Small ribosomal subunit protein uS4y
BL: Small ribosomal subunit protein uS17z
BN: Small ribosomal subunit protein uS15y
cS: Small ribosomal subunit protein uS11x
BV: Small ribosomal subunit protein eS21z
BW: Small ribosomal subunit protein uS8z/uS8w
BX: Small ribosomal subunit protein uS12y
BY: Small ribosomal subunit protein eS24z
BZ: Small ribosomal subunit protein eS26x
Bb: Small ribosomal subunit protein eS27y
Be: Small ribosomal subunit protein eS30z/eS30y/eS30x
Cn: Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v
hetero molecules


Theoretical massNumber of molelcules
Total (without water)942,67638
Polymers942,15320
Non-polymers52318
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 9

#1: RNA chain 18S RNA


Mass: 581965.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: GenBank: X16077.1

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Small ribosomal subunit protein ... , 19 types, 19 molecules BABBBCBEBGBHBIBJBLBNcSBVBWBXBYBZBbBeCn

#2: Protein Small ribosomal subunit protein uS2y / 40S ribosomal protein Sa-2 / p40 protein homolog


Mass: 30682.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8H173
#3: Protein Small ribosomal subunit protein eS1z / 40S ribosomal protein S3a-1


Mass: 29906.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9CAV0
#4: Protein Small ribosomal subunit protein uS5w / 40S ribosomal protein S2-4


Mass: 30169.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SCM3
#5: Protein Small ribosomal subunit protein eS4z / 40S ribosomal protein S4-1


Mass: 29862.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q93VH9
#6: Protein Small ribosomal subunit protein eS6y / 40S ribosomal protein S6-2 / Protein EMBRYO DEFECTIVE 3010


Mass: 28228.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P51430
#7: Protein Small ribosomal subunit protein eS7z / 40S ribosomal protein S7-1


Mass: 21964.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C514
#8: Protein Small ribosomal subunit protein eS8z / 40S ribosomal protein S8-1


Mass: 25047.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q93VG5
#9: Protein Small ribosomal subunit protein uS4y / 40S ribosomal protein S9-2


Mass: 23207.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FLF0
#10: Protein Small ribosomal subunit protein uS17z / 40S ribosomal protein S11-1 / Protein EMBRYO DEFECTIVE 1080


Mass: 17996.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P16181
#11: Protein Small ribosomal subunit protein uS15y / 40S ribosomal protein S13-2


Mass: 17123.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P59224
#12: Protein Small ribosomal subunit protein uS11x / 40S ribosomal protein S14-3


Mass: 16268.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P42036
#13: Protein Small ribosomal subunit protein eS21z / 40S ribosomal protein S21-1


Mass: 9086.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M337
#14: Protein Small ribosomal subunit protein uS8z/uS8w / 40S ribosomal protein S15a-1


Mass: 14829.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P42798
#15: Protein Small ribosomal subunit protein uS12y / 40S ribosomal protein S23-2 / S12


Mass: 15770.618 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49201
#16: Protein Small ribosomal subunit protein eS24z / 40S ribosomal protein S24-1


Mass: 15412.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SS17
#17: Protein Small ribosomal subunit protein eS26x / 40S ribosomal protein S26-3


Mass: 14662.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LYK9
#18: Protein Small ribosomal subunit protein eS27y / 40S ribosomal protein S27-2


Mass: 9614.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M2F1
#19: Protein Small ribosomal subunit protein eS30z/eS30y/eS30x / 40S ribosomal protein S30


Mass: 6910.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49689
#20: Protein/peptide Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v / 60S ribosomal protein L41 / Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62120

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Non-polymers , 3 types, 18 molecules

#21: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: 60S LSU Arabidopsis (root) ribosome complex / Type: RIBOSOME / Entity ID: #1-#20 / Source: NATURAL
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis (plant)
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
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: 105000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115070 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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