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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 / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / 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. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S27e signature. / Ribosomal protein S6, eukaryotic / 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 S17, archaeal/eukaryotic / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S8e / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / 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 S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / 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 / Ribosomal S11, conserved site / Ribosomal protein S11 signature.
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: To Be Published
Title: Cryo-EM structure of the Arabidopsis thaliana ribosome in translating and non-translating states
Authors: Karki, S. / Paavilainen, V.
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
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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